X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 289.0
Details BuphA.00051.b.B1.PS37982 at 35 mg/mL against MCSG1 screen condition E4, 0.2 M Li2SO4, 0.1 M Tris pH 8.5, 25% PEG 3350 supplemented with 20% EG as cryo-protectant

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.39 α = 90
b = 103.84 β = 90
c = 55.47 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2016-08-18
Diffraction Radiation
Monochromator Protocol
-- 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
2.4 50 99.7 0.062 -- -- 3.5 -- 6748 -- -3.0 47.44
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)
2.4 2.46 100.0 0.567 -- 3.75 -- --

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 2.401 37.906 -- 1.35 -- 6743 707 99.7 -- 0.2086 0.2012 0.2693 --
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 2.4007 2.586 -- 116 1203 0.2703 0.3495 -- 100.0
X Ray Diffraction 2.586 2.8462 -- 145 1175 0.247 0.3242 -- 100.0
X Ray Diffraction 2.8462 3.2578 -- 153 1185 0.2308 0.2945 -- 100.0
X Ray Diffraction 3.2578 4.1037 -- 151 1198 0.1982 0.2606 -- 100.0
X Ray Diffraction 4.1037 37.9106 -- 142 1275 0.1737 0.2419 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 62.383
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.054
f_bond_d 0.007
f_dihedral_angle_d 15.627
f_angle_d 0.85
f_plane_restr 0.006
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1065
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 11

Software

Software
Software Name Purpose
XSCALE data scaling
MOLREP phasing
PHENIX refinement version: dev_2499
PDB_EXTRACT data extraction version: 3.20
XDS data reduction
MOLREP phasing