X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 15% PEG3350, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.72 α = 90
b = 86.72 β = 90
c = 120.01 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2007-08-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.97893 NSLS X4C

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
2.5 30 100.0 0.107 -- -- 2.6 -- 34855 -- -- --
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)
2.5 2.59 100.0 0.457 -- -- 2.6 3488

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
-- 2.5 30.0 -- 0.0 -- 34814 1750 99.92 -- 0.198 0.195 0.251 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 2.502 2.566 -- 123 2438 0.27 0.317 -- 99.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.211
Anisotropic B[1][1] 0.9
Anisotropic B[1][2] 0.45
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.36
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.167
r_scangle_it 1.815
r_dihedral_angle_3_deg 17.553
r_mcbond_it 0.471
r_dihedral_angle_4_deg 19.282
r_bond_refined_d 0.01
r_mcangle_it 0.767
r_symmetry_vdw_refined 0.238
r_dihedral_angle_1_deg 8.598
r_nbtor_refined 0.305
r_scbond_it 1.12
r_gen_planes_refined 0.004
r_dihedral_angle_2_deg 35.334
r_nbd_refined 0.205
r_chiral_restr 0.094
r_angle_refined_deg 1.297
r_xyhbond_nbd_refined 0.207
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6865
Nucleic Acid Atoms 0
Heterogen Atoms 21
Solvent Atoms 216

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.004
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing