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 347 with the SMILES code OC1=NC(=NC2=CC=CC=C12)C(=O)NCC1CC1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.25 α = 90
b = 73 β = 109.42
c = 52.75 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
CCD MARMOSAIC 225 mm CCD -- 2014-06-04
Diffraction Radiation
Monochromator Protocol
-- 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
1.22 42.68 98.6 0.051 -- -- 4.143 -- 94816 -- -3.0 10.05
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 97.0 0.625 -- 2.18 -- --

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 29.43 -- 1.36 -- 94813 4740 98.68 -- 0.1326 0.1317 0.1498 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 1.2195 1.2333 -- 152 2885 0.2192 0.2131 -- 95.0
X Ray Diffraction 1.2333 1.2478 -- 154 2933 0.2026 0.2389 -- 98.0
X Ray Diffraction 1.2478 1.2631 -- 158 2997 0.2006 0.2562 -- 98.0
X Ray Diffraction 1.2631 1.279 -- 153 2913 0.1966 0.198 -- 98.0
X Ray Diffraction 1.279 1.2959 -- 158 2993 0.1861 0.241 -- 98.0
X Ray Diffraction 1.2959 1.3136 -- 154 2941 0.178 0.1872 -- 98.0
X Ray Diffraction 1.3136 1.3324 -- 157 2986 0.1623 0.1926 -- 98.0
X Ray Diffraction 1.3324 1.3523 -- 158 3000 0.1559 0.1961 -- 98.0
X Ray Diffraction 1.3523 1.3734 -- 156 2953 0.1488 0.1923 -- 98.0
X Ray Diffraction 1.3734 1.3959 -- 157 2977 0.1413 0.1679 -- 98.0
X Ray Diffraction 1.3959 1.42 -- 157 2986 0.1355 0.176 -- 98.0
X Ray Diffraction 1.42 1.4458 -- 156 2961 0.1298 0.1716 -- 98.0
X Ray Diffraction 1.4458 1.4736 -- 158 3019 0.1224 0.1646 -- 98.0
X Ray Diffraction 1.4736 1.5037 -- 158 3003 0.1214 0.1687 -- 99.0
X Ray Diffraction 1.5037 1.5364 -- 157 2979 0.1097 0.1341 -- 99.0
X Ray Diffraction 1.5364 1.5721 -- 159 3015 0.1038 0.1341 -- 99.0
X Ray Diffraction 1.5721 1.6115 -- 158 3000 0.0982 0.127 -- 99.0
X Ray Diffraction 1.6115 1.655 -- 157 2990 0.1008 0.1258 -- 99.0
X Ray Diffraction 1.655 1.7037 -- 159 3025 0.0987 0.1158 -- 99.0
X Ray Diffraction 1.7037 1.7587 -- 160 3031 0.0986 0.1315 -- 99.0
X Ray Diffraction 1.7587 1.8215 -- 160 3031 0.098 0.1248 -- 99.0
X Ray Diffraction 1.8215 1.8945 -- 159 3031 0.1009 0.1157 -- 100.0
X Ray Diffraction 1.8945 1.9807 -- 159 3016 0.101 0.1222 -- 100.0
X Ray Diffraction 1.9807 2.0851 -- 160 3037 0.1033 0.1231 -- 100.0
X Ray Diffraction 2.0851 2.2157 -- 160 3055 0.1063 0.1344 -- 100.0
X Ray Diffraction 2.2157 2.3867 -- 161 3060 0.1183 0.1237 -- 100.0
X Ray Diffraction 2.3867 2.6267 -- 160 3031 0.1287 0.1404 -- 100.0
X Ray Diffraction 2.6267 3.0065 -- 161 3069 0.1378 0.1403 -- 100.0
X Ray Diffraction 3.0065 3.7866 -- 162 3073 0.1489 0.155 -- 100.0
X Ray Diffraction 3.7866 29.4382 -- 162 3083 0.1619 0.1667 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.4508
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.198
f_plane_restr 0.006
f_dihedral_angle_d 10.584
f_chiral_restr 0.071
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 240

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