X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop with Microseeding
pH 7.7
Temperature 294.0
Details Polyethylene glycol 4000, 25% MgCl2, 200 mM Ethylene glycol, 30% Sodium HEPES, 100 mM, pH 7.7, vapor diffusion, hanging drop, with microseeding, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.5 α = 90
b = 84.5 β = 90
c = 86.47 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-02-13
IMAGE PLATE RIGAKU RAXIS IV -- 1999-03-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.9802,0.9800,0.9537 ALS 5.0.1
SYNCHROTRON NSLS BEAMLINE X4A -- NSLS X4A

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 38 99.7 0.091 -- -- 3.72 23567 23496 0.0 0.0 15.9
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)
2.0 2.07 99.4 0.624 -- -- 3.48 2322

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
-- 2.0 33.7 0.0 0.0 46649 43560 4205 93.8 0.264 0.264 0.264 0.292 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 2.0 2.07 -- 265 3056 0.375 0.38 0.023 71.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 34.1
Anisotropic B[1][1] -3.76
Anisotropic B[1][2] 0.87
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.52
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.65
c_bond_d 0.007
c_dihedral_angle_d 22.6
c_improper_angle_d 0.75
c_mcbond_it 1.35
c_mcangle_it 2.23
c_scbond_it 1.77
c_angle_deg 1.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.35
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.36
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2662
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 116

Software

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