X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 3.5
Temperature 277.0
Details 50mM sodium acetate 3.5, 0.75M sodium chloride, 30% ethylene glycol, 11.25% polyethylene glycol 400

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.86 α = 90
b = 79.86 β = 90
c = 38.02 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI JUNGFRAU 1M -- 2017-07-15
Diffraction Radiation
Monochromator Protocol
-- LAUE
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID09 0.8058-0.8262 ESRF ID09

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
1.84 28.24 100.0 -- -- -- 162.8 -- 11142 -- -- --
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)
1.84 1.906 -- -- -- -- -- --

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 1.84 28.235 -- 1.34 -- 11140 1097 99.95 -- 0.1587 0.156 0.1831 --
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 1.84 1.9237 -- 132 1221 0.1954 0.2362 0.0 100.0
X Ray Diffraction 1.9237 2.0251 -- 134 1224 0.1703 0.236 0.0 100.0
X Ray Diffraction 2.0251 2.152 -- 135 1229 0.1424 0.1796 0.0 100.0
X Ray Diffraction 2.152 2.3181 -- 134 1229 0.1429 0.1806 0.0 100.0
X Ray Diffraction 2.3181 2.5512 -- 136 1252 0.1517 0.1837 0.0 100.0
X Ray Diffraction 2.5512 2.92 -- 138 1251 0.1523 0.1902 0.0 100.0
X Ray Diffraction 2.92 3.6777 -- 139 1279 0.1524 0.1767 0.0 100.0
X Ray Diffraction 3.6777 28.2381 -- 149 1358 0.1581 0.1689 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.2993
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.049
f_angle_d 0.807
f_bond_d 0.007
f_plane_restr 0.004
f_dihedral_angle_d 10.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 81

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1-2155_9999
PDB_EXTRACT data extraction version: 3.24
CrystFEL data reduction version: 0.6.3
CrystFEL data scaling version: 0.8.0
PHASER phasing
Coot model building