X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details Crystallization solution: 1.33 M LiSO4, 0.1 M Tris pH 8.5. 1:1 ratio (250 nL: 250 nL) of precipitant to protein (at a concentration of 13.9 mg/ml). 60 mcL reservoir. Protein purification buffer 50mM Tris-HCl, 150 mM NaCl; pH 7.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.96 α = 90
b = 108.96 β = 90
c = 82.74 γ = 120
Symmetry
Space Group P 64 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX300HE -- 2014-08-14
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.99 APS 21-ID-D

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
2.3 80 94.3 0.084 -- 31.34 14.8 -- 12398 -- -- --
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)
2.3 2.38 64.7 0.432 0.432 1.9 7.1 --

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 2.31 80.0 -- 0.0 -- 11792 604 94.04 -- 0.1692 0.1676 0.2025 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 2.312 2.372 -- 27 534 0.278 0.312 -- 59.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 81.78
Anisotropic B[1][1] 0.68
Anisotropic B[1][2] 0.34
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.2
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 40.102
r_chiral_restr 0.071
r_gen_planes_refined 0.005
r_bond_other_d 0.001
r_dihedral_angle_3_deg 13.36
r_angle_other_deg 0.899
r_dihedral_angle_4_deg 10.807
r_bond_refined_d 0.008
r_angle_refined_deg 1.253
r_gen_planes_other 0.001
r_mcbond_other 13.629
r_dihedral_angle_1_deg 5.678
r_mcbond_it 13.696
r_mcangle_it 14.363
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 861
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 113

Software

Software
Software Name Purpose
PDB_EXTRACT data extraction version: 3.15
REFMAC refinement version: 5.8.0103
SBC-Collect data collection
HKL-3000 phasing
SCALEPACK data scaling
PHENIX model building
HKL-3000 data reduction
Coot model building