X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 277.0
Details 100 mM Na acetate pH 5.0, 13% isopropanol, and 200 mM CaCl2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 367.26 α = 90
b = 367.26 β = 90
c = 187.07 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2014-02-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.97857 APS 21-ID-D

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
8.69 30 98.8 0.189 -- 8.233 5.1 -- 7324 -- -- --
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)
8.7 8.85 94.8 0.529 -- -- 4.8 365

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 8.69 30.0 -- 0.0 -- 6954 367 94.22 -- 0.2105 0.2096 0.2286 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 8.691 8.897 -- 26 332 0.302 0.307 -- 66.42
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 359.555
Anisotropic B[1][1] -1.92
Anisotropic B[1][2] -0.96
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.22
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.006
r_angle_refined_deg 1.17
r_chiral_restr 0.086
r_dihedral_angle_4_deg 12.762
r_dihedral_angle_3_deg 14.454
r_dihedral_angle_1_deg 5.729
r_mcbond_it 6.938
r_mcangle_it 12.791
r_mcbond_other 6.937
r_gen_planes_other 0.003
r_bond_other_d 0.002
r_gen_planes_refined 0.006
r_dihedral_angle_2_deg 28.359
r_angle_other_deg 0.866
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12044
Nucleic Acid Atoms 0
Heterogen Atoms 368
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0073
HKL-2000 data reduction
SCALEPACK data scaling
Aimless data scaling
PHASER phasing
PDB_EXTRACT data extraction version: 3.15