X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 291.0
Details 0.1 M HEPES pH 7.5, 25% PEG3350.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.4 α = 90
b = 65.4 β = 90
c = 180.86 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2016-01-09
Diffraction Radiation
Monochromator Protocol
double crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U1 1.2818 SSRF BL17U1

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
2.65 50 99.9 0.088 -- -- 11.0 -- 12074 -- -- 65.77
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)
2.65 2.7 100.0 1.075 -- -- 11.0 --

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 2.655 37.193 -- 1.36 -- 12003 605 99.71 -- 0.1965 0.1935 0.2514 --
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 2.6546 2.9217 -- 144 2754 0.2336 0.3317 0.0 99.0
X Ray Diffraction 2.9217 3.3442 -- 146 2799 0.2194 0.2935 0.0 100.0
X Ray Diffraction 3.3442 4.2124 -- 157 2838 0.1975 0.2569 0.0 100.0
X Ray Diffraction 4.2124 37.1967 -- 158 3007 0.178 0.2244 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 74.48
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.044
f_plane_restr 0.007
f_bond_d 0.009
f_chiral_restr 0.055
f_dihedral_angle_d 19.063
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2290
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 7

Software

Software
Software Name Purpose
PHENIX refinement version: dev_2689
DENZO data collection
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.22