X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 290.0
Details Molecular Dimensions Morpheus screen G7: 10% PEG 4000, 20% Glycerol, 20mM of each: Na-formate, Ammonium-acetate, Trisodium citrate, Na/K tartrate, Na oxamate; 100mM MOPS/NaHEPES pH 7.5; BumuA.00020.x.B1.PS37849 at 20mg/ml + 2mM NADP; cryo: direct, puck pfb1-6, tray 271259 g7

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.08 α = 90
b = 87.03 β = 90
c = 124.59 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2016-03-31
Diffraction Radiation
Monochromator Protocol
Diamond [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G

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
1.2 50 100.0 0.08 -- -- 8.0 -- 147035 -- -3.0 8.27
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)
1.2 1.23 100.0 0.551 -- 3.32 -- --

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 1.2 50.0 -- 1.35 -- 147020 1964 99.98 -- 0.113 0.1128 0.1297 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 1.2 1.23 -- 157 10226 0.1537 0.1678 -- 100.0
X Ray Diffraction 1.23 1.2633 -- 153 10249 0.1371 0.1606 -- 100.0
X Ray Diffraction 1.2633 1.3005 -- 168 10274 0.1286 0.1657 -- 100.0
X Ray Diffraction 1.3005 1.3424 -- 124 10292 0.1221 0.1375 -- 100.0
X Ray Diffraction 1.3424 1.3904 -- 115 10370 0.1166 0.144 -- 100.0
X Ray Diffraction 1.3904 1.4461 -- 176 10218 0.1037 0.1199 -- 100.0
X Ray Diffraction 1.4461 1.5119 -- 132 10344 0.096 0.1376 -- 100.0
X Ray Diffraction 1.5119 1.5916 -- 159 10308 0.0925 0.1207 -- 100.0
X Ray Diffraction 1.5916 1.6914 -- 174 10261 0.0947 0.1159 -- 100.0
X Ray Diffraction 1.6914 1.8219 -- 82 10450 0.0985 0.1293 -- 100.0
X Ray Diffraction 1.8219 2.0053 -- 126 10369 0.1021 0.1249 -- 100.0
X Ray Diffraction 2.0053 2.2955 -- 128 10458 0.1024 0.1289 -- 100.0
X Ray Diffraction 2.2955 2.8919 -- 109 10482 0.1116 0.1171 -- 100.0
X Ray Diffraction 2.8919 43.8152 -- 161 10755 0.129 0.1262 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.7957
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.035
f_angle_d 1.064
f_plane_restr 0.008
f_chiral_restr 0.082
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3607
Nucleic Acid Atoms 0
Heterogen Atoms 112
Solvent Atoms 687

Software

Software
Software Name Purpose
XDS data scaling
XSCALE data scaling
PHASER phasing
Coot model building
PHENIX model building
PHENIX refinement
PDB_EXTRACT data extraction