X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 291.0
Details 100 mM sodium cacodylate, 12% PEG 2,000 MME, 3% PEG 200, 1% cis-inositol, 20% glycerol, 1 mM rifamycin CGP 4832, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 172.82 α = 90
b = 172.82 β = 90
c = 87.91 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR MARRESEARCH -- 1999-07-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ELETTRA BEAMLINE 5.2R -- ELETTRA 5.2R

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
2.9 30 99.9 0.072 -- -- 4.83 -- 33363 1.0 1.0 23.2
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)
2.9 3.08 99.8 0.246 -- -- 4.83 33363

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
-- 2.9 30.0 0.0 0.0 -- 33363 1542 99.0 -- 0.233 0.233 0.275 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 2.9 3.08 -- 201 5307 0.329 0.387 0.027 99.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 68.4
Anisotropic B[1][1] -16.26
Anisotropic B[1][2] -0.94
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -16.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 32.52
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 4.25
c_mcbond_it 2.75
c_bond_d 0.008
c_mcangle_it 4.29
c_scangle_it 5.96
c_improper_angle_d 0.92
c_angle_deg 1.5
c_dihedral_angle_d 25.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.46
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.5
Luzzati Sigma A (R-Free Set) 0.58
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5523
Nucleic Acid Atoms 0
Heterogen Atoms 328
Solvent Atoms 179

Software

Software
Software Name Purpose
DENZO data reduction
XDS data reduction
CNS refinement
XDS data scaling
CNS phasing