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 154 with the SMILES code O=C(NC1=NC2=CC=CC=C2S1)[C@H]1CCS(=O)(=O)C1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.21 α = 90
b = 73.19 β = 109.21
c = 52.54 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
1.25 42.69 99.0 0.06 -- -- 3.736 -- 88482 -- -3.0 9.49
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)
1.25 1.33 95.4 0.382 -- 2.8 -- --

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 1.249 42.695 -- 1.99 -- 88482 4425 99.08 -- 0.1383 0.1373 0.1559 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 1.2493 1.2635 -- 125 2373 0.1791 0.2326 -- 83.0
X Ray Diffraction 1.2635 1.2784 -- 140 2659 0.1737 0.1955 -- 96.0
X Ray Diffraction 1.2784 1.294 -- 149 2831 0.1565 0.186 -- 100.0
X Ray Diffraction 1.294 1.3104 -- 147 2787 0.1565 0.1868 -- 100.0
X Ray Diffraction 1.3104 1.3276 -- 149 2831 0.1465 0.1826 -- 100.0
X Ray Diffraction 1.3276 1.3458 -- 148 2805 0.138 0.1689 -- 100.0
X Ray Diffraction 1.3458 1.365 -- 148 2823 0.1404 0.1684 -- 100.0
X Ray Diffraction 1.365 1.3854 -- 149 2817 0.1332 0.1646 -- 100.0
X Ray Diffraction 1.3854 1.407 -- 148 2822 0.1334 0.1632 -- 100.0
X Ray Diffraction 1.407 1.4301 -- 146 2778 0.1325 0.1657 -- 100.0
X Ray Diffraction 1.4301 1.4548 -- 149 2828 0.1289 0.171 -- 100.0
X Ray Diffraction 1.4548 1.4812 -- 146 2774 0.1215 0.177 -- 100.0
X Ray Diffraction 1.4812 1.5097 -- 151 2863 0.1207 0.1579 -- 100.0
X Ray Diffraction 1.5097 1.5405 -- 147 2801 0.1137 0.1503 -- 100.0
X Ray Diffraction 1.5405 1.574 -- 148 2808 0.1148 0.144 -- 100.0
X Ray Diffraction 1.574 1.6107 -- 149 2822 0.1094 0.1384 -- 100.0
X Ray Diffraction 1.6107 1.6509 -- 147 2798 0.112 0.1376 -- 100.0
X Ray Diffraction 1.6509 1.6956 -- 150 2846 0.1127 0.1401 -- 100.0
X Ray Diffraction 1.6956 1.7455 -- 148 2820 0.115 0.1512 -- 100.0
X Ray Diffraction 1.7455 1.8018 -- 148 2806 0.1136 0.1556 -- 100.0
X Ray Diffraction 1.8018 1.8662 -- 147 2808 0.1136 0.158 -- 100.0
X Ray Diffraction 1.8662 1.9409 -- 150 2837 0.1103 0.127 -- 100.0
X Ray Diffraction 1.9409 2.0293 -- 148 2817 0.1069 0.1193 -- 100.0
X Ray Diffraction 2.0293 2.1362 -- 149 2834 0.1093 0.1267 -- 100.0
X Ray Diffraction 2.1362 2.2701 -- 150 2844 0.1132 0.135 -- 100.0
X Ray Diffraction 2.2701 2.4453 -- 148 2819 0.1291 0.1381 -- 100.0
X Ray Diffraction 2.4453 2.6914 -- 150 2839 0.1414 0.1453 -- 100.0
X Ray Diffraction 2.6914 3.0807 -- 149 2839 0.1478 0.1369 -- 100.0
X Ray Diffraction 3.0807 3.881 -- 149 2839 0.1618 0.1731 -- 100.0
X Ray Diffraction 3.881 42.7197 -- 153 2889 0.1883 0.1922 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.5737
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.19
f_plane_restr 0.006
f_bond_d 0.006
f_chiral_restr 0.073
f_dihedral_angle_d 10.655
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 201

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