X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 298.0
Details Protein (20 mM Hepes, pH 8.0, 500 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (10% PEG3350, 100mM pottasium iodide); Cryoprotection (30% PEG400 and 25% saturated ammonium sulfate), Vapor Diffusion, Sitting Drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 134.6 α = 90
b = 134.6 β = 90
c = 234.79 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 ADSC QUANTUM 315 MIRRORS 2012-03-15
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.9792 NSLS X29A

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
3.25 50 100.0 -- 0.136 -- 8.4 64698 64698 -- 0.0 78.0
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)
3.25 3.29 100.0 -- 0.969 2.6 8.4 2186

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 3.25 47.76 -- 0.0 -- 34573 1930 99.61 -- 0.1905 0.1875 0.2431 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 3.254 3.338 -- 148 2331 0.265 0.34 -- 98.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 85.2254
Anisotropic B[1][1] 2.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.29
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.005
r_angle_refined_deg 1.755
r_angle_other_deg 0.885
r_dihedral_angle_4_deg 18.688
r_chiral_restr 0.085
r_dihedral_angle_3_deg 16.906
r_bond_refined_d 0.014
r_dihedral_angle_1_deg 7.228
r_dihedral_angle_2_deg 39.478
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6923
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 6

Software

Software
Software Name Purpose
REFMAC refinement version: 5.7.0025
PDB_EXTRACT data extraction version: 3.11
CBASS data collection
HKL-2000 data reduction
SCALEPACK data scaling
PHENIX phasing