X-RAY DIFFRACTION Experimental Data & Validation


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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 = 92.7 α = 90
b = 92.7 β = 90
c = 131.1 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 2010-06-25
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
1.28 50 97.0 -- 0.065 -- 10.7 83248 83248 -- -- --
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)
1.28 1.3 99.1 -- 0.378 5.2 9.0 4180

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 1.28 34.232 -- 0.0 84816 80710 4106 94.12 0.1065 0.1065 0.1054 0.127 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 1.2801 1.2951 -- 161 2524 0.1412 0.1603 -- 91.0
X Ray Diffraction 1.2951 1.3109 -- 123 2502 0.1334 0.1701 -- 92.0
X Ray Diffraction 1.3109 1.3275 -- 122 2605 0.1237 0.1839 -- 93.0
X Ray Diffraction 1.3275 1.345 -- 134 2495 0.1218 0.1434 -- 92.0
X Ray Diffraction 1.345 1.3634 -- 135 2602 0.1143 0.1702 -- 93.0
X Ray Diffraction 1.3634 1.3829 -- 141 2596 0.1017 0.1461 -- 93.0
X Ray Diffraction 1.3829 1.4035 -- 137 2541 0.1043 0.1376 -- 93.0
X Ray Diffraction 1.4035 1.4254 -- 131 2676 0.0947 0.1063 -- 95.0
X Ray Diffraction 1.4254 1.4488 -- 138 2609 0.0934 0.1208 -- 95.0
X Ray Diffraction 1.4488 1.4738 -- 140 2621 0.0934 0.1211 -- 95.0
X Ray Diffraction 1.4738 1.5006 -- 144 2627 0.0893 0.1112 -- 94.0
X Ray Diffraction 1.5006 1.5295 -- 159 2592 0.0854 0.1218 -- 95.0
X Ray Diffraction 1.5295 1.5607 -- 127 2654 0.0861 0.1231 -- 95.0
X Ray Diffraction 1.5607 1.5946 -- 153 2629 0.0815 0.1077 -- 96.0
X Ray Diffraction 1.5946 1.6317 -- 159 2649 0.0785 0.1076 -- 96.0
X Ray Diffraction 1.6317 1.6725 -- 151 2673 0.0792 0.101 -- 95.0
X Ray Diffraction 1.6725 1.7177 -- 155 2643 0.0778 0.0965 -- 95.0
X Ray Diffraction 1.7177 1.7683 -- 152 2627 0.0832 0.1086 -- 96.0
X Ray Diffraction 1.7683 1.8253 -- 159 2688 0.0829 0.1083 -- 96.0
X Ray Diffraction 1.8253 1.8906 -- 135 2680 0.0818 0.113 -- 95.0
X Ray Diffraction 1.8906 1.9663 -- 146 2648 0.0891 0.0917 -- 96.0
X Ray Diffraction 1.9663 2.0558 -- 135 2721 0.0922 0.1124 -- 96.0
X Ray Diffraction 2.0558 2.1641 -- 136 2713 0.093 0.1208 -- 96.0
X Ray Diffraction 2.1641 2.2997 -- 140 2698 0.0955 0.1247 -- 95.0
X Ray Diffraction 2.2997 2.4772 -- 124 2703 0.1043 0.1131 -- 94.0
X Ray Diffraction 2.4772 2.7264 -- 134 2715 0.1115 0.139 -- 94.0
X Ray Diffraction 2.7264 3.1207 -- 144 2673 0.1157 0.1384 -- 94.0
X Ray Diffraction 3.1207 3.9308 -- 148 2726 0.1258 0.1551 -- 93.0
X Ray Diffraction 3.9308 34.2441 -- 143 2774 0.1459 0.141 -- 89.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.1894
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.1894
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.3787
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.088
f_dihedral_angle_d 13.51
f_angle_d 1.353
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2432
Nucleic Acid Atoms 0
Heterogen Atoms 73
Solvent Atoms 481

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