X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 297.0
Details 0.1M HEPES:NaOH pH 7.5, 1.4M Sodium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.48 α = 90
b = 64.91 β = 100.68
c = 56.57 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-07-08
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97931, 0.97945 APS 19-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
1.37 50 95.8 0.1 -- -- 4.6 30480 30480 -- -3.0 16.4
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)
1.37 1.39 92.5 0.351 -- -- 3.9 1467

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 1.37 18.45 -- 0.0 30373 30373 1541 95.76 0.1196 0.1196 0.1175 0.1587 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 1.37 1.405 -- 107 2061 0.162 0.206 -- 93.13
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.4968
Anisotropic B[1][1] -0.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.65
Anisotropic B[2][2] 0.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.3
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 11.727
r_sphericity_free 38.871
r_bond_refined_d 0.015
r_bond_other_d 0.001
r_angle_refined_deg 1.689
r_angle_other_deg 0.881
r_dihedral_angle_1_deg 6.188
r_dihedral_angle_2_deg 33.307
r_dihedral_angle_3_deg 12.548
r_dihedral_angle_4_deg 17.185
r_chiral_restr 0.113
r_gen_planes_refined 0.009
r_gen_planes_other 0.002
r_rigid_bond_restr 3.763
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1283
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 277

Software

Computing
Computing Package Purpose
SBC-Collect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL-3000, SHELXD, SHELXE, MLPHARE, DM, SOLVE/RESOLVE, ARP/WARP, CCP4, O, COOT Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
HKL data reduction