X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details Bis-Tris, Li2SO4, PEG-3350, pH 5.5, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.99 α = 90
b = 77.99 β = 90
c = 64.7 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2008-07-12
Diffraction Radiation
Monochromator Protocol
Kohzu HLD-4 Double Crystal SAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-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
1.39 67.57 100.0 0.057 -- -- 5.3 -- 88640 -- -- --
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)
1.39 1.44 100.0 0.496 -- -- 3.9 8881

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
SAD 1.39 67.57 -- 0.0 -- 84088 4437 99.89 -- 0.1736 0.1724 0.1962 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 1.39 1.426 -- 306 6230 0.266 0.255 -- 99.48
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.2237
Anisotropic B[1][1] -0.09
Anisotropic B[1][2] -0.05
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.14
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.492
r_dihedral_angle_3_deg 11.302
r_gen_planes_refined 0.006
r_dihedral_angle_2_deg 33.287
r_dihedral_angle_4_deg 19.709
r_bond_refined_d 0.008
r_chiral_restr 0.083
r_angle_refined_deg 1.359
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3306
Nucleic Acid Atoms 0
Heterogen Atoms 167
Solvent Atoms 509

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing version: 2.03
REFMAC refinement version: 5.6.0117
PDB_EXTRACT data extraction version: 3.10