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 272 with the SMILES code CN1N=C(C)C(CC(=O)NC2=CC=CC=N2)=C1C

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.4 α = 90
b = 73.14 β = 109.65
c = 52.87 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 -- 2013-07-18
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
1.47 42.76 93.5 0.049 -- -- 2.338 -- 51878 -- -3.0 11.17
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)
1.47 1.56 91.7 0.277 -- 3.52 -- --

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 1.469 42.759 -- 1.36 -- 51876 2589 93.59 -- 0.1402 0.1386 0.1699 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 1.469 1.4972 -- 138 2611 0.1895 0.2242 -- 90.0
X Ray Diffraction 1.4972 1.5278 -- 143 2697 0.1779 0.2357 -- 93.0
X Ray Diffraction 1.5278 1.561 -- 145 2691 0.1741 0.2409 -- 92.0
X Ray Diffraction 1.561 1.5973 -- 139 2686 0.157 0.2329 -- 92.0
X Ray Diffraction 1.5973 1.6373 -- 138 2659 0.1436 0.174 -- 91.0
X Ray Diffraction 1.6373 1.6815 -- 138 2674 0.1315 0.1967 -- 91.0
X Ray Diffraction 1.6815 1.731 -- 142 2705 0.1256 0.1753 -- 93.0
X Ray Diffraction 1.731 1.7869 -- 145 2755 0.112 0.1798 -- 94.0
X Ray Diffraction 1.7869 1.8508 -- 147 2776 0.1112 0.167 -- 96.0
X Ray Diffraction 1.8508 1.9249 -- 147 2792 0.1091 0.1353 -- 95.0
X Ray Diffraction 1.9249 2.0125 -- 149 2793 0.1086 0.1513 -- 95.0
X Ray Diffraction 2.0125 2.1186 -- 145 2785 0.1149 0.15 -- 95.0
X Ray Diffraction 2.1186 2.2513 -- 144 2754 0.1207 0.1572 -- 94.0
X Ray Diffraction 2.2513 2.4251 -- 142 2721 0.1325 0.1673 -- 93.0
X Ray Diffraction 2.4251 2.6691 -- 148 2792 0.1409 0.1722 -- 95.0
X Ray Diffraction 2.6691 3.0553 -- 147 2793 0.1453 0.1575 -- 95.0
X Ray Diffraction 3.0553 3.8489 -- 147 2794 0.1531 0.1814 -- 94.0
X Ray Diffraction 3.8489 42.7772 -- 145 2809 0.159 0.1519 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.2783
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 10.805
f_bond_d 0.008
f_chiral_restr 0.07
f_plane_restr 0.006
f_angle_d 1.166
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 195

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