X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 291.0
Details 28% PEG-2000, 0.1 M Bis-Tris, pH 6.5, vapor diffusion, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.2 α = 90
b = 27.5 β = 101.01
c = 58.85 γ = 90
Symmetry
Space Group I 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-12-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97911 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
1.33 39.52 99.7 -- 0.05 -- 4.0 16885 16885 -- -- --
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)
1.33 1.4 99.9 0.958 0.958 0.8 4.0 2468

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 1.33 39.52 -- 0.0 -- 16884 818 99.66 -- 0.1621 0.1593 0.2215 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 1.33 1.365 -- 49 1193 0.288 0.302 -- 99.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.3337
Anisotropic B[1][1] -0.61
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.97
Anisotropic B[2][2] -1.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.54
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 15.885
r_sphericity_free 43.092
r_rigid_bond_restr 3.691
r_mcangle_it 4.655
r_mcbond_other 3.507
r_bond_refined_d 0.016
r_bond_other_d 0.001
r_angle_refined_deg 1.735
r_angle_other_deg 0.858
r_dihedral_angle_1_deg 6.654
r_dihedral_angle_2_deg 33.36
r_dihedral_angle_3_deg 11.384
r_dihedral_angle_4_deg 11.67
r_chiral_restr 0.105
r_gen_planes_refined 0.01
r_gen_planes_other 0.001
r_mcbond_it 4.051
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 601
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 50

Software

Computing
Computing Package Purpose
sbccollect Data Collection
xds Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
phaser Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.7.0032 refinement
Phaser molecular replacement
SCALA version: 3.3.20 data reduction