X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 277.0
Details 2.40M ammonium sulfate, 0.1M Bicine pH 9.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.77 α = 90
b = 70.77 β = 90
c = 67.47 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 MARMOSAIC 325 mm CCD Vertical focusing mirror; double crystal Si(111) monochromator 2015-02-04
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL14-1 0.9792 SSRL BL14-1

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
1.8 28.65 100.0 0.08 -- -- 6.17 -- 16483 -- -3.0 21.665
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)
1.8 1.86 100.0 0.739 -- 1.9 -- --

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
SAD 1.8 28.652 -- 0.0 -- 16437 832 99.99 -- 0.1743 0.1732 0.1947 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 1.8 1.92 -- 145 2768 0.1972 0.2274 -- 99.99
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.9582
Anisotropic B[1][1] -0.2102
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.2102
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.4204
RMS Deviations
Key Refinement Restraint Deviation
t_omega_torsion 2.64
t_bond_d 0.01
t_other_torsion 2.51
t_angle_deg 0.84
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.202
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1236
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 184

Software

Software
Software Name Purpose
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XDS data scaling version: November 3, 2014 BUILT=20141118
BUSTER-TNT refinement version: 2.10.2
XSCALE data scaling
SHELXD phasing
BUSTER refinement version: 2.10.2