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 235 with the SMILES code CC1=CC(=O)N2N=C(NCC3=CC=CC=C3F)SC2=N1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.32 α = 90
b = 73.13 β = 109.43
c = 52.71 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
1.27 42.74 99.1 0.051 -- -- 3.743 -- 85123 -- -3.0 10.26
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)
1.27 1.34 96.7 0.501 -- 2.49 -- --

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 1.268 42.739 -- 2.0 -- 85123 4257 99.24 -- 0.1384 0.1374 0.1584 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 1.2677 1.2821 -- 125 2367 0.2201 0.2455 -- 88.0
X Ray Diffraction 1.2821 1.2972 -- 141 2687 0.1931 0.216 -- 99.0
X Ray Diffraction 1.2972 1.313 -- 140 2652 0.1842 0.1991 -- 99.0
X Ray Diffraction 1.313 1.3296 -- 142 2706 0.1732 0.1909 -- 99.0
X Ray Diffraction 1.3296 1.3471 -- 141 2679 0.1731 0.2337 -- 99.0
X Ray Diffraction 1.3471 1.3656 -- 143 2701 0.1614 0.1723 -- 99.0
X Ray Diffraction 1.3656 1.3851 -- 141 2688 0.1517 0.1865 -- 99.0
X Ray Diffraction 1.3851 1.4058 -- 141 2678 0.1508 0.1738 -- 99.0
X Ray Diffraction 1.4058 1.4277 -- 143 2712 0.1366 0.1536 -- 100.0
X Ray Diffraction 1.4277 1.4512 -- 141 2679 0.1334 0.1559 -- 99.0
X Ray Diffraction 1.4512 1.4762 -- 141 2689 0.1283 0.1665 -- 100.0
X Ray Diffraction 1.4762 1.503 -- 142 2689 0.1239 0.1522 -- 100.0
X Ray Diffraction 1.503 1.5319 -- 142 2692 0.1228 0.1464 -- 100.0
X Ray Diffraction 1.5319 1.5632 -- 143 2721 0.1188 0.1518 -- 100.0
X Ray Diffraction 1.5632 1.5972 -- 142 2708 0.1136 0.1604 -- 100.0
X Ray Diffraction 1.5972 1.6344 -- 143 2711 0.1062 0.153 -- 100.0
X Ray Diffraction 1.6344 1.6752 -- 143 2709 0.1055 0.1417 -- 100.0
X Ray Diffraction 1.6752 1.7205 -- 141 2691 0.1028 0.1211 -- 100.0
X Ray Diffraction 1.7205 1.7711 -- 143 2708 0.1057 0.1238 -- 100.0
X Ray Diffraction 1.7711 1.8283 -- 143 2726 0.1057 0.1329 -- 100.0
X Ray Diffraction 1.8283 1.8937 -- 143 2705 0.1077 0.145 -- 100.0
X Ray Diffraction 1.8937 1.9695 -- 143 2734 0.1057 0.1154 -- 100.0
X Ray Diffraction 1.9695 2.0591 -- 143 2701 0.1057 0.1078 -- 100.0
X Ray Diffraction 2.0591 2.1677 -- 142 2711 0.1081 0.1338 -- 100.0
X Ray Diffraction 2.1677 2.3035 -- 143 2708 0.1194 0.1431 -- 100.0
X Ray Diffraction 2.3035 2.4813 -- 144 2731 0.1268 0.1601 -- 100.0
X Ray Diffraction 2.4813 2.731 -- 143 2735 0.144 0.1549 -- 100.0
X Ray Diffraction 2.731 3.1261 -- 144 2719 0.1438 0.1647 -- 100.0
X Ray Diffraction 3.1261 3.9381 -- 144 2735 0.1602 0.1759 -- 100.0
X Ray Diffraction 3.9381 42.7631 -- 147 2794 0.1802 0.1861 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.3247
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_angle_d 1.177
f_chiral_restr 0.07
f_dihedral_angle_d 10.625
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 204

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