Masquerade: removing non-sample scattering from integrated reflection intensities

X-ray diffraction experiments at very low temperatures require samples to be isolated from atmospheric conditions and held under vacuum. These conditions are usually maintained via the use of beryllium chambers, which also scatter X-rays, causing unwanted contamination of the sample's diffraction pattern. The removal of this contamination requires novel data-collection and processing procedures to be employed. Herein a new approach is described, which utilizes the differences in origin of scattering vectors from the sample and the beryllium to eliminate non-sample scattering. The program Masquerade has been written to remove contaminated regions of the diffraction data from the processing programs. Coupled with experiments at different detector distances, it allows for the acquisition of decontaminated data. Studies of several single crystals have shown that this approach increases data quality, highlighted by the improvement in internal agreement factor with the test case of cytidine presented herein.

Computing details

Data collection: Apex II (Bruker, 2010); cell refinement: Apex II (Bruker, 2010); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: XS, G.M. Sheldrick, Acta Cryst. (2008). A64, 112-122; program(s) used to refine structure: XL, G.M. Sheldrick, Acta Cryst. (2008). A64, 112-122; molecular graphics: O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann, OLEX2: a complete structure solution, refinement and analysis program. J. Appl. Cryst. (2009). 42, 339-341.; software used to prepare material for publication: O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann, OLEX2: a complete structure solution, refinement and analysis program. J. Appl. Cryst. (2009). 42, 339-341..

Figures

(cytidine_2k)

Crystal data

C9H13N3O5	F(000) = 512
Mr = 243.22	Dx = 1.556 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
a = 5.0784 (3) Å	µ = 0.13 mm^−1
b = 13.9046 (10) Å	T = 2 K
c = 14.6992 (10) Å	Needle, clear colourless
V = 1037.96 (12) Å^3	0.26 × 0.05 × 0.05 mm
Z = 4

Data collection

Bruker APEX-II CCD diffractometer	2456 independent reflections
Radiation source: Bruker TXS with Helios Optics, Rotating Anode	1916 reflections with I > 2σ(I)
Multilayer optics monochromator	Rint = 0.052
Detector resolution: 8.3333 pixels mm^-1	θmax = 29.5°, θmin = 2.0°
φ scans	h = −6→5
Absorption correction: multi-scan SADABS2008/1 (Bruker,2008) was used for absorption correction. R(int) was 0.0761 before and 0.0570 after correction. The Ratio of minimum to maximum transmission is 0.8445. The λ/2 correction factor is 0.0015.	k = −19→19
Tmin = 0.365, Tmax = 0.432	l = −20→20
9630 measured reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.046	H-atom parameters constrained
wR(F^2) = 0.090	w = 1/[σ^2(Fo^2) + (0.0431P)^2 + 0.0504P] where P = (Fo^2 + 2Fc^2)/3
S = 1.03	(Δ/σ)max < 0.001
2456 reflections	Δρmax = 0.29 e Å^−3
157 parameters	Δρmin = −0.24 e Å^−3
0 restraints	Absolute structure: Not refined as all light-atom structure
Primary atom site location: structure-invariant direct methods

Special details

Experimental. Data were collected using φ scans of 0.5 degree width at 20 second exposures. Data were collected at 2 Kelvin, resulting in the Alert C in the CIF report.

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Completeness value resulting in Alert A is due to constraints on the experimental data collection parameters, the reduction in data completeness forms a significant result in the paper and is highlighted therein

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O4	0.0496 (4)	0.67555 (11)	0.44839 (8)	0.0117 (4)
H4	0.0239	0.6560	0.3950	0.018*
N1	0.1182 (4)	0.46426 (12)	0.67742 (10)	0.0082 (4)
O5	−0.1453 (3)	0.41486 (10)	0.42909 (9)	0.0121 (4)
H5	−0.0444	0.4305	0.3863	0.018*
N2	0.4615 (4)	0.40068 (13)	0.76938 (10)	0.0093 (4)
O3	−0.0475 (3)	0.71677 (10)	0.63188 (8)	0.0109 (4)
H3	−0.1203	0.7403	0.5857	0.016*
C5	−0.0654 (5)	0.54615 (15)	0.66010 (12)	0.0089 (5)
H5A	−0.1363	0.5708	0.7191	0.011*
O2	−0.2749 (3)	0.51363 (10)	0.60459 (8)	0.0091 (3)
N3	0.6470 (4)	0.25597 (13)	0.73486 (10)	0.0123 (4)
H3A	0.7533	0.2638	0.7816	0.015*
H3B	0.6586	0.2038	0.7012	0.015*
O1	0.2930 (3)	0.54968 (10)	0.79465 (8)	0.0103 (3)
C1	0.2956 (5)	0.47393 (15)	0.74938 (12)	0.0095 (5)
C2	0.4694 (5)	0.32267 (15)	0.71530 (12)	0.0100 (5)
C8	−0.2618 (5)	0.55944 (14)	0.51559 (12)	0.0088 (5)
H8	−0.3876	0.6147	0.5141	0.011*
C9	−0.3374 (5)	0.48805 (15)	0.44212 (12)	0.0103 (5)
H9A	−0.5072	0.4577	0.4586	0.012*
H9B	−0.3630	0.5230	0.3841	0.012*
C7	0.0187 (5)	0.59789 (15)	0.51006 (12)	0.0090 (5)
H7	0.1406	0.5445	0.4926	0.011*
C4	0.1191 (5)	0.38328 (15)	0.62465 (12)	0.0103 (5)
H4A	−0.0035	0.3775	0.5761	0.012*
C3	0.2917 (5)	0.31144 (15)	0.64051 (12)	0.0115 (5)
H3C	0.2950	0.2555	0.6034	0.014*
C6	0.0735 (5)	0.62804 (14)	0.60846 (12)	0.0093 (5)
H6	0.2667	0.6291	0.6216	0.011*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O4	0.0160 (10)	0.0124 (8)	0.0067 (6)	−0.0011 (7)	0.0004 (6)	0.0010 (5)
N1	0.0072 (12)	0.0076 (9)	0.0098 (7)	0.0009 (7)	−0.0004 (7)	0.0014 (6)
O5	0.0141 (11)	0.0108 (8)	0.0115 (6)	0.0008 (7)	0.0036 (6)	−0.0003 (5)
N2	0.0098 (12)	0.0095 (9)	0.0085 (7)	0.0001 (8)	0.0004 (7)	−0.0002 (6)
O3	0.0142 (11)	0.0089 (7)	0.0094 (6)	0.0031 (7)	−0.0015 (6)	−0.0003 (5)
C5	0.0068 (14)	0.0105 (11)	0.0094 (8)	0.0003 (8)	−0.0006 (8)	−0.0006 (7)
O2	0.0072 (10)	0.0120 (7)	0.0082 (6)	−0.0013 (6)	−0.0004 (6)	0.0023 (5)
N3	0.0165 (14)	0.0100 (9)	0.0105 (7)	0.0026 (8)	−0.0007 (7)	−0.0008 (6)
O1	0.0116 (10)	0.0099 (8)	0.0095 (6)	0.0004 (6)	−0.0012 (6)	−0.0017 (5)
C1	0.0085 (15)	0.0126 (11)	0.0074 (8)	−0.0015 (9)	0.0033 (8)	0.0023 (7)
C2	0.0100 (15)	0.0100 (11)	0.0100 (8)	−0.0044 (9)	0.0021 (8)	0.0037 (7)
C8	0.0095 (14)	0.0090 (10)	0.0078 (7)	0.0005 (9)	0.0008 (8)	0.0019 (7)
C9	0.0103 (15)	0.0121 (11)	0.0086 (8)	−0.0008 (9)	0.0011 (9)	−0.0001 (7)
C7	0.0119 (15)	0.0075 (10)	0.0076 (8)	−0.0001 (9)	0.0010 (8)	−0.0008 (7)
C4	0.0100 (14)	0.0126 (11)	0.0082 (8)	−0.0029 (8)	−0.0005 (8)	0.0004 (7)
C3	0.0157 (16)	0.0094 (11)	0.0096 (8)	−0.0023 (9)	−0.0010 (8)	−0.0007 (7)
C6	0.0105 (14)	0.0089 (11)	0.0084 (8)	0.0010 (8)	−0.0001 (8)	−0.0015 (7)

Geometric parameters (Å, º)

O4—C7	1.419 (2)	C5—C6	1.540 (3)
N1—C5	1.493 (3)	O2—C8	1.456 (2)
N1—C1	1.396 (3)	N3—C2	1.325 (3)
N1—C4	1.367 (2)	O1—C1	1.246 (2)
O5—C9	1.423 (3)	C2—C3	1.431 (3)
N2—C1	1.354 (3)	C8—C9	1.516 (3)
N2—C2	1.345 (3)	C8—C7	1.524 (3)
O3—C6	1.421 (3)	C7—C6	1.531 (2)
C5—O2	1.415 (3)	C4—C3	1.349 (3)
C1—N1—C5	117.29 (15)	N3—C2—C3	121.31 (19)
C4—N1—C5	122.24 (17)	O2—C8—C9	110.00 (15)
C4—N1—C1	120.46 (18)	O2—C8—C7	104.13 (16)
C2—N2—C1	119.77 (18)	C9—C8—C7	115.36 (17)
N1—C5—C6	111.22 (18)	O5—C9—C8	113.00 (19)
O2—C5—N1	108.91 (16)	O4—C7—C8	113.87 (17)
O2—C5—C6	107.25 (15)	O4—C7—C6	112.03 (16)
C5—O2—C8	110.11 (15)	C8—C7—C6	102.46 (16)
N2—C1—N1	119.59 (17)	C3—C4—N1	120.9 (2)
O1—C1—N1	118.64 (18)	C4—C3—C2	117.49 (19)
O1—C1—N2	121.76 (18)	O3—C6—C5	108.94 (18)
N2—C2—C3	121.5 (2)	O3—C6—C7	112.82 (17)
N3—C2—N2	117.15 (19)	C7—C6—C5	100.36 (16)