X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 6.5
Temperature 298.0
Details 17% MPD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 402.3 α = 90
b = 402.3 β = 90
c = 176.4 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
PIXEL DECTRIS PILATUS 6M -- 2017-04-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.98 SSRL BL12-2

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
3.45 39.22 100.0 -- -- -- 384.7 -- 188443 -- -- 83.59
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)
3.45 3.6318 -- -- -- -- -- --

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 3.45 39.223 -- 1.33 -- 188443 1013 99.97 -- 0.219 0.2187 0.272 --
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 3.45 3.6318 -- 142 26462 0.3448 0.4065 0.0 100.0
X Ray Diffraction 3.6318 3.8591 -- 144 26506 0.3027 0.3566 0.0 100.0
X Ray Diffraction 3.8591 4.1568 -- 144 26586 0.2539 0.2983 0.0 100.0
X Ray Diffraction 4.1568 4.5745 -- 144 26645 0.2219 0.299 0.0 100.0
X Ray Diffraction 4.5745 5.2351 -- 144 26736 0.1865 0.2357 0.0 100.0
X Ray Diffraction 5.2351 6.5907 -- 146 26902 0.1738 0.2458 0.0 100.0
X Ray Diffraction 6.5907 39.2254 -- 149 27593 0.1731 0.2067 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 87.8496
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_angle_d 0.851
f_chiral_restr 0.042
f_bond_d 0.004
f_dihedral_angle_d 18.876
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19107
Nucleic Acid Atoms 32940
Heterogen Atoms 808
Solvent Atoms 0

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing
PHENIX refinement
PDB_EXTRACT data extraction version: 3.24
CrystFEL data reduction