X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 1.9 M cesium chloride, 50% DMSO, 50 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.1 α = 90
b = 93.1 β = 90
c = 130.9 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 Collimating Mirror 2010-06-25
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.38 50 98.6 -- 0.067 -- 5.8 68072 68072 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.38 1.4 99.9 -- 0.5 3.4 5.9 3373

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.381 22.302 -- 0.0 68231 64916 3315 94.11 0.1107 0.1107 0.1091 0.1402 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.381 1.401 -- 120 2348 0.163 0.2128 -- 87.0
X Ray Diffraction 1.401 1.4219 -- 134 2394 0.1362 0.171 -- 89.0
X Ray Diffraction 1.4219 1.4442 -- 112 2415 0.1304 0.1844 -- 90.0
X Ray Diffraction 1.4442 1.4678 -- 162 2453 0.1238 0.1803 -- 92.0
X Ray Diffraction 1.4678 1.4931 -- 117 2486 0.1166 0.1692 -- 92.0
X Ray Diffraction 1.4931 1.5203 -- 125 2445 0.1034 0.1519 -- 91.0
X Ray Diffraction 1.5203 1.5495 -- 154 2488 0.0986 0.147 -- 93.0
X Ray Diffraction 1.5495 1.5811 -- 133 2536 0.0899 0.1413 -- 94.0
X Ray Diffraction 1.5811 1.6155 -- 148 2513 0.0915 0.1363 -- 94.0
X Ray Diffraction 1.6155 1.6531 -- 142 2556 0.0863 0.1663 -- 95.0
X Ray Diffraction 1.6531 1.6944 -- 121 2589 0.0878 0.125 -- 95.0
X Ray Diffraction 1.6944 1.7402 -- 133 2543 0.0839 0.1229 -- 95.0
X Ray Diffraction 1.7402 1.7914 -- 141 2611 0.0873 0.1254 -- 96.0
X Ray Diffraction 1.7914 1.8492 -- 137 2533 0.0848 0.1135 -- 94.0
X Ray Diffraction 1.8492 1.9152 -- 125 2557 0.0937 0.1251 -- 94.0
X Ray Diffraction 1.9152 1.9919 -- 161 2605 0.0951 0.1284 -- 97.0
X Ray Diffraction 1.9919 2.0824 -- 133 2679 0.0963 0.1242 -- 98.0
X Ray Diffraction 2.0824 2.1921 -- 135 2662 0.0912 0.1098 -- 97.0
X Ray Diffraction 2.1921 2.3294 -- 144 2653 0.0961 0.1352 -- 96.0
X Ray Diffraction 2.3294 2.509 -- 146 2652 0.1069 0.1262 -- 97.0
X Ray Diffraction 2.509 2.7611 -- 146 2648 0.1094 0.1425 -- 96.0
X Ray Diffraction 2.7611 3.1596 -- 141 2694 0.1112 0.144 -- 96.0
X Ray Diffraction 3.1596 3.9771 -- 145 2725 0.1236 0.1309 -- 96.0
X Ray Diffraction 3.9771 22.3047 -- 160 2816 0.145 0.165 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.1688
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.1688
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.3376
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.089
f_dihedral_angle_d 14.07
f_angle_d 1.275
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2428
Nucleic Acid Atoms 0
Heterogen Atoms 70
Solvent Atoms 474

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
PHASER model building
MAR345dtb data collection