X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 290.0
Details 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystal obtained by streak-seeding and soaked with 90 mM of fragment 187 with the SMILES code COC(=O)C[C@H]1CCCO1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.25 α = 90
b = 73.25 β = 109.19
c = 52.67 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2013-04-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1

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
1.22 42.73 93.4 0.061 -- -- 3.826 -- 90144 -- -3.0 9.36
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)
1.22 1.29 75.6 0.283 -- 3.63 -- --

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 1.219 42.732 -- 2.0 -- 90142 4508 93.53 -- 0.1231 0.1226 0.1332 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 1.2194 1.2333 -- 95 1798 0.1514 0.157 -- 59.0
X Ray Diffraction 1.2333 1.2478 -- 105 2002 0.1373 0.1551 -- 66.0
X Ray Diffraction 1.2478 1.263 -- 118 2231 0.1362 0.1729 -- 74.0
X Ray Diffraction 1.263 1.279 -- 141 2678 0.1315 0.1562 -- 88.0
X Ray Diffraction 1.279 1.2958 -- 150 2858 0.1206 0.1624 -- 94.0
X Ray Diffraction 1.2958 1.3136 -- 152 2875 0.1126 0.1484 -- 95.0
X Ray Diffraction 1.3136 1.3324 -- 153 2919 0.1094 0.1322 -- 95.0
X Ray Diffraction 1.3324 1.3523 -- 153 2913 0.1042 0.1379 -- 96.0
X Ray Diffraction 1.3523 1.3734 -- 152 2871 0.1064 0.1357 -- 96.0
X Ray Diffraction 1.3734 1.3959 -- 153 2918 0.1021 0.118 -- 96.0
X Ray Diffraction 1.3959 1.42 -- 154 2932 0.1069 0.1216 -- 96.0
X Ray Diffraction 1.42 1.4458 -- 153 2891 0.1023 0.134 -- 96.0
X Ray Diffraction 1.4458 1.4736 -- 156 2964 0.1005 0.116 -- 96.0
X Ray Diffraction 1.4736 1.5037 -- 155 2958 0.0974 0.1248 -- 96.0
X Ray Diffraction 1.5037 1.5364 -- 153 2901 0.0982 0.1214 -- 96.0
X Ray Diffraction 1.5364 1.5721 -- 156 2970 0.0962 0.1334 -- 97.0
X Ray Diffraction 1.5721 1.6114 -- 156 2955 0.0959 0.1084 -- 97.0
X Ray Diffraction 1.6114 1.655 -- 155 2942 0.097 0.1364 -- 97.0
X Ray Diffraction 1.655 1.7037 -- 155 2958 0.0964 0.1283 -- 97.0
X Ray Diffraction 1.7037 1.7587 -- 158 3000 0.1001 0.1059 -- 98.0
X Ray Diffraction 1.7587 1.8216 -- 157 2981 0.1007 0.1146 -- 98.0
X Ray Diffraction 1.8216 1.8945 -- 157 2978 0.1036 0.1118 -- 98.0
X Ray Diffraction 1.8945 1.9807 -- 157 2985 0.1014 0.1127 -- 98.0
X Ray Diffraction 1.9807 2.0851 -- 158 2995 0.1004 0.116 -- 98.0
X Ray Diffraction 2.0851 2.2158 -- 158 3011 0.104 0.103 -- 98.0
X Ray Diffraction 2.2158 2.3868 -- 159 3017 0.1133 0.1239 -- 99.0
X Ray Diffraction 2.3868 2.627 -- 158 3003 0.1268 0.1412 -- 99.0
X Ray Diffraction 2.627 3.0071 -- 160 3036 0.1338 0.1288 -- 99.0
X Ray Diffraction 3.0071 3.7882 -- 159 3033 0.148 0.1428 -- 98.0
X Ray Diffraction 3.7882 42.7583 -- 162 3061 0.1807 0.1745 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.275
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 10.665
f_chiral_restr 0.072
f_bond_d 0.006
f_plane_restr 0.006
f_angle_d 1.217
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 218

Software

Software
Software Name Purpose
XDS data scaling
PHENIX refinement
PHASER phasing version: 2.5.7
PDB_EXTRACT data extraction version: 3.20
XDS data reduction