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 50 mM Tris, 1.9 M cesium chloride, 50% DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.8 α = 90
b = 92.8 β = 90
c = 130.1 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 2010-10-20
Diffraction Radiation
Monochromator Protocol
Double Crystal 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
1.41 50 99.8 -- 0.062 -- 4.7 64097 64097 -- -- --
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)
1.41 1.43 100.0 -- 0.494 3.0 4.6 3131

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 1.41 31.683 -- 0.0 63974 60892 3082 94.96 0.1277 0.1277 0.1263 0.1531 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 1.41 1.432 -- 136 2332 0.1737 0.211 -- 86.0
X Ray Diffraction 1.432 1.4555 -- 121 2433 0.1647 0.2116 -- 89.0
X Ray Diffraction 1.4555 1.4806 -- 133 2424 0.152 0.2063 -- 90.0
X Ray Diffraction 1.4806 1.5075 -- 135 2438 0.1528 0.217 -- 90.0
X Ray Diffraction 1.5075 1.5365 -- 143 2469 0.1364 0.1857 -- 91.0
X Ray Diffraction 1.5365 1.5679 -- 128 2548 0.1235 0.1743 -- 92.0
X Ray Diffraction 1.5679 1.602 -- 141 2528 0.1137 0.1616 -- 93.0
X Ray Diffraction 1.602 1.6392 -- 151 2539 0.1109 0.1621 -- 94.0
X Ray Diffraction 1.6392 1.6802 -- 129 2589 0.1114 0.1622 -- 94.0
X Ray Diffraction 1.6802 1.7257 -- 133 2622 0.1089 0.1729 -- 95.0
X Ray Diffraction 1.7257 1.7764 -- 128 2596 0.1028 0.1514 -- 95.0
X Ray Diffraction 1.7764 1.8338 -- 156 2600 0.098 0.1657 -- 95.0
X Ray Diffraction 1.8338 1.8993 -- 132 2639 0.1065 0.1324 -- 95.0
X Ray Diffraction 1.8993 1.9753 -- 137 2682 0.113 0.1492 -- 97.0
X Ray Diffraction 1.9753 2.0652 -- 150 2720 0.1188 0.1556 -- 99.0
X Ray Diffraction 2.0652 2.1741 -- 139 2731 0.1113 0.1351 -- 99.0
X Ray Diffraction 2.1741 2.3103 -- 144 2737 0.1092 0.1301 -- 99.0
X Ray Diffraction 2.3103 2.4886 -- 157 2737 0.1189 0.1689 -- 99.0
X Ray Diffraction 2.4886 2.7389 -- 148 2772 0.1297 0.151 -- 99.0
X Ray Diffraction 2.7389 3.1349 -- 138 2812 0.1319 0.1402 -- 99.0
X Ray Diffraction 3.1349 3.9485 -- 158 2846 0.131 0.13 -- 99.0
X Ray Diffraction 3.9485 31.691 -- 145 3016 0.1526 0.1511 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.0575
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.0575
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.115
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.074
f_dihedral_angle_d 12.935
f_angle_d 1.05
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2428
Nucleic Acid Atoms 0
Heterogen Atoms 71
Solvent Atoms 450

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