X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 296.0
Details 0.1M sodium/potassium phosphate, 30% 2-methyl-2,4-pentanediol, pH 6.0, vapor diffusion, hanging drop, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.85 α = 90
b = 117.85 β = 90
c = 76.02 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2012-03-23
Diffraction Radiation
Monochromator Protocol
Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C

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
2.79 100 99.5 0.087 -- -- 12.9 -- 9715 -- -- --
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)
2.79 2.9 97.5 0.602 -- -- 6.1 937

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 2.79 60.97 -- 0.0 -- 9710 468 99.35 -- 0.2178 0.2154 0.2671 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 2.79 2.863 -- 33 633 0.366 0.375 -- 95.69
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 99.336
Anisotropic B[1][1] -3.65
Anisotropic B[1][2] -1.83
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.86
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.007
r_mcangle_it 6.947
r_angle_other_deg 1.446
r_bond_other_d 0.007
r_dihedral_angle_3_deg 19.281
r_dihedral_angle_2_deg 39.611
r_chiral_restr 0.091
r_dihedral_angle_1_deg 5.67
r_mcbond_other 4.505
r_gen_planes_other 0.005
r_mcbond_it 4.506
r_bond_refined_d 0.011
r_dihedral_angle_4_deg 18.741
r_angle_refined_deg 1.602
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2637
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 4

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.8.0049
PDB_EXTRACT data extraction version: 3.14