X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 290.0
Details RigakuReagents JCSG+ screen A6: 20% PEG 1000, 200mM Li2SO4, 50mM Na2HPO4/Citric acid pH4.2; BuxeA.00027.j.B1.PS37826 at 15mg/ml + 2.5mM CoA; cryo: 15% EG + 1mM CoA in 2 steps; tray 270711a6; puck vod9-4

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.3 α = 90
b = 73.75 β = 99.66
c = 149.49 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 RAYONIX MX-225 -- 2016-03-25
Diffraction Radiation
Monochromator Protocol
Diamond [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
1.5 50 99.5 0.06 -- -- 4.5 -- 266729 -- -3.0 14.02
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)
1.5 1.54 94.5 0.528 -- 2.19 -- --

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 1.5 45.004 -- 1.34 -- 266691 1958 99.49 -- 0.13 0.1298 0.1601 --
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 1.5 1.5376 -- 137 17878 0.1945 0.2521 -- 94.0
X Ray Diffraction 1.5376 1.5791 -- 134 18834 0.1616 0.2143 -- 100.0
X Ray Diffraction 1.5791 1.6256 -- 139 18898 0.1462 0.19 -- 100.0
X Ray Diffraction 1.6256 1.6781 -- 167 18933 0.1333 0.1856 -- 100.0
X Ray Diffraction 1.6781 1.7381 -- 130 18952 0.123 0.15 -- 100.0
X Ray Diffraction 1.7381 1.8076 -- 124 18890 0.1183 0.1896 -- 100.0
X Ray Diffraction 1.8076 1.8899 -- 127 19015 0.1169 0.1564 -- 100.0
X Ray Diffraction 1.8899 1.9896 -- 148 18978 0.116 0.1643 -- 100.0
X Ray Diffraction 1.9896 2.1142 -- 143 18975 0.1139 0.129 -- 100.0
X Ray Diffraction 2.1142 2.2774 -- 137 18924 0.1124 0.1549 -- 100.0
X Ray Diffraction 2.2774 2.5066 -- 142 19018 0.1236 0.1332 -- 100.0
X Ray Diffraction 2.5066 2.8693 -- 135 19044 0.1324 0.1678 -- 100.0
X Ray Diffraction 2.8693 3.6147 -- 141 19111 0.1374 0.1617 -- 100.0
X Ray Diffraction 3.6147 45.0241 -- 154 19283 0.1343 0.1524 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.6833
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.798
f_bond_d 0.005
f_dihedral_angle_d 14.36
f_chiral_restr 0.047
f_plane_restr 0.005
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11493
Nucleic Acid Atoms 0
Heterogen Atoms 277
Solvent Atoms 1791

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
MOLREP phasing
PHENIX model building
Coot model building
PHENIX refinement version: dev_2386
PDB_EXTRACT data extraction