X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 277.0
Details 20.0% Glycerol, 1.6M NH4H2PO3, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.59 α = 90
b = 79.59 β = 90
c = 237.38 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Flat collimating mirror, toroid focusing mirror 2004-07-18
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 -- SSRL BL9-2

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
1.93 44.97 85.3 -- 0.071 -- 5.3 -- 18980 -- -- 16.512

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 1.93 44.972 -- 0.0 -- 18940 981 100.0 -- 0.168 0.166 0.202 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 1.93 1.98 -- 32 496 0.296 0.368 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.477
Anisotropic B[1][1] 0.33
Anisotropic B[1][2] 0.16
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.49
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.471
r_mcbond_it 0.869
r_dihedral_angle_3_deg 11.84
r_scangle_it 1.84
r_mcbond_other 0.16
r_mcangle_it 1.526
r_angle_other_deg 0.98
r_bond_other_d 0.001
r_dihedral_angle_4_deg 15.928
r_chiral_restr 0.098
r_dihedral_angle_1_deg 3.075
r_gen_planes_refined 0.006
r_scbond_it 1.068
r_bond_refined_d 0.015
r_dihedral_angle_2_deg 35.174
r_gen_planes_other 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1786
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 187

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0102
PHENIX refinement
MolProbity model building version: 3beta29
SCALA data scaling version: 3.3.15
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction
MOLREP phasing