X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 297.0
Details 0.2 M Li2SO4, 0.1 M HEPES/NaOH pH 7.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.19 α = 90
b = 58.19 β = 90
c = 94.78 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2012-10-22
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97915 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
1.3 30 99.7 0.086 -- -- 9.0 46523 46401 -- -3.0 14.0
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)
1.3 1.32 100.0 0.848 -- 2.7 8.9 2297

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 1.3 22.25 -- -- 46401 46401 1177 99.5 0.15991 0.15991 0.15897 0.19843 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 1.299 1.333 -- 81 3283 0.213 0.234 -- 99.73
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 14.766
Anisotropic B[1][1] 0.16
Anisotropic B[1][2] 0.08
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.24
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 1.473
r_scangle_it 5.641
r_scbond_it 3.69
r_mcangle_it 2.864
r_mcbond_other 0.5
r_bond_refined_d 0.017
r_bond_other_d 0.001
r_angle_refined_deg 1.569
r_angle_other_deg 0.935
r_dihedral_angle_1_deg 6.139
r_dihedral_angle_2_deg 32.042
r_dihedral_angle_3_deg 11.857
r_dihedral_angle_4_deg 16.782
r_chiral_restr 0.094
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_mcbond_it 1.793
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1556
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 174

Software

Computing
Computing Package Purpose
SBCcollect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
SHELX, MLPHARE, DM, Buccaneer, ARP/WARP, COOT Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
COOT model building
ARP/WARP model building
Buccaneer model building
DM model building
MLPHARE model building
SHELX model building
SBCcollect data collection