X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 295.0
Details The Classics II Suite, condition 22, mixed 1:1 v/v with protein sample (7.3 mg/mL, 0.25M NaCl, 5mM BME, 10mM Tris/HCl pH 8.3), pH 7.0, VAPOR DIFFUSION, temperature 295K, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.39 α = 90
b = 77.4 β = 90
c = 81.5 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD beryllium lenses 2008-10-02
Diffraction Radiation
Monochromator Protocol
single diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
1.82 30 98.3 0.051 -- -- 5.5 37963 37963 -- -3.0 --
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)
1.82 1.86 91.8 0.543 -- 2.58 4.9 --

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 1.824 28.89 -- -- 36019 36019 1901 98.16 -- 0.18635 0.18431 0.22479 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 1.824 1.871 2432 129 2424 0.242 0.281 -- 90.44
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 32.486
Anisotropic B[1][1] -0.53
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.16
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.687
r_scbond_it 2.949
r_mcangle_it 1.908
r_mcbond_other 0.343
r_bond_refined_d 0.011
r_bond_other_d 0.002
r_angle_refined_deg 1.289
r_angle_other_deg 0.779
r_dihedral_angle_1_deg 3.844
r_dihedral_angle_2_deg 31.68
r_dihedral_angle_3_deg 10.925
r_dihedral_angle_4_deg 10.126
r_chiral_restr 0.085
r_gen_planes_refined 0.004
r_gen_planes_other 0.001
r_mcbond_it 1.087
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2906
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 272

Software

Computing
Computing Package Purpose
Blue Max Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
Phaser Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0102 refinement
Phaser model building
Blue version: Max data collection