X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 298.0
Details 100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.35 α = 90
b = 119.84 β = 95.89
c = 109.42 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97924 APS 19-BM

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
3.1 37.5 -- -- -- -- -- -- 38826 -- -- --

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
-- 3.1 37.5 -- 0.0 -- 33878 1726 90.31 -- 0.225 0.221 0.302 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 3.1 3.267 -- 213 3859 0.327 0.403 -- 75.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 75.25
Anisotropic B[1][1] 1.29
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.35
Anisotropic B[2][2] 0.99
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.38
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_free 4.538
r_scbond_it 1.444
r_angle_refined_deg 1.293
r_rigid_bond_restr 1.258
r_mcbond_it 1.187
r_dihedral_angle_2_deg 42.386
r_nbd_refined 0.259
r_symmetry_vdw_refined 0.27
r_dihedral_angle_4_deg 20.556
r_gen_planes_refined 0.004
r_symmetry_hbond_refined 0.358
r_chiral_restr 0.084
r_dihedral_angle_1_deg 4.844
r_xyhbond_nbd_refined 0.15
r_nbtor_refined 0.322
r_sphericity_bonded 0.686
r_bond_refined_d 0.011
r_dihedral_angle_3_deg 18.757
r_mcangle_it 2.113
r_scangle_it 2.173
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12522
Nucleic Acid Atoms 0
Heterogen Atoms 94
Solvent Atoms 27

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.005