X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 12-16% PEG 6000, 0.1 M Tris-HCl pH 8.0, 0.5 M LiCl, 12.5% glycerol, and 5% PEG-400, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.28 α = 90
b = 75.28 β = 90
c = 179.85 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- 2011-08
Diffraction Radiation
Monochromator Protocol
-- MULTIPLE WAVELENGTH ANOMALOUS SCATTERING
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
synchrotron APS Beamline 23 ID 0.97935,0.97954, 0.94936 APS 23 ID

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
3 100 99.7 0.083 -- -- 9.4 -- 11051 -- -- --
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)
3.0 3.05 100.0 0.77 -- 2.8 9.7 --

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
MAD 3.0 45.809 -- 0.79 -- 10958 1097 99.76 -- 0.2699 0.2674 0.2916 --
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 3.0001 3.1366 -- 134 1210 0.3684 0.4302 -- 100.0
X Ray Diffraction 3.1366 3.3019 -- 132 1188 0.3327 0.4064 -- 100.0
X Ray Diffraction 3.3019 3.5087 -- 135 1205 0.2975 0.3093 -- 100.0
X Ray Diffraction 3.5087 3.7795 -- 135 1223 0.2721 0.3105 -- 100.0
X Ray Diffraction 3.7795 4.1596 -- 135 1210 0.2418 0.2456 -- 100.0
X Ray Diffraction 4.1596 4.761 -- 137 1239 0.2217 0.2358 -- 100.0
X Ray Diffraction 4.761 5.9962 -- 139 1251 0.2892 0.3181 -- 100.0
X Ray Diffraction 5.9962 45.8142 -- 150 1335 0.2373 0.2547 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.8312
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.8312
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.6623
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.001
f_chiral_restr 0.036
f_dihedral_angle_d 15.263
f_angle_d 0.553
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2675
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
RESOLVE density modification
SOLVE phasing
HKL data reduction