X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details PEG 4000, Magnesium chloride, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.62 α = 90
b = 102.62 β = 90
c = 128.48 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 4 -- 2000-05-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.979 NSLS X9B

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
1.75 20 99.7 -- 0.054 -- 6.5 513786 78938 0.0 0.0 10.3
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)
1.75 1.81 99.8 -- 0.217 8.3 5.5 7823

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 1.75 20.0 1.4 2.0 77969 75787 7608 95.6 -- 0.191 0.189 0.212 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 1.75 1.86 10575 1095 10575 0.193 0.226 0.007 89.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Restrained
Mean Isotropic B 14.2
Anisotropic B[1][1] -1.62
Anisotropic B[1][2] -0.55
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.62
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.25
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.93
c_mcbond_it 0.6
c_scangle_it 1.61
c_bond_d 0.005
c_dihedral_angle_d 24.1
c_mcangle_it 0.99
c_angle_deg 1.4
c_scbond_it 1.05
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.06
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.1
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5688
Nucleic Acid Atoms 0
Heterogen Atoms 72
Solvent Atoms 485

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 0.9
DENZO data reduction
SCALEPACK data scaling