X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 298.0
Details 30% PEG4K, 0.2M Sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.68 α = 90
b = 88.84 β = 92.75
c = 230.52 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2009-08-28
CCD ADSC QUANTUM 315 mirrors 2009-08-27
Diffraction Radiation
Monochromator Protocol
SI-III SINGLE WAVELENGTH
SI-III SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 0.9791 NSLS X25
SYNCHROTRON NSLS BEAMLINE X12C 0.9791 NSLS X12C

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
2.31 50 98.1 0.065 -- -- 3.6 99100 99100 -- -- 29.7
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)
2.31 2.35 87.8 0.165 -- 4.0 2.7 4458

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 2.31 48.31 -- 0.0 99100 97059 2940 96.6 -- 0.224 0.224 0.274 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 2.31 2.45 -- 481 14861 0.28 0.34 0.015 91.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 36.0
Anisotropic B[1][1] 2.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.62
Anisotropic B[2][2] 4.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.17
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.52
c_scbond_it 1.79
c_mcangle_it 1.67
c_mcbond_it 1.11
c_improper_angle_d 0.88
c_dihedral_angle_d 23.5
c_angle_deg 1.5
c_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.39
Luzzati Sigma A (R-Free Set) 0.38
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16759
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 395

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
ShelxD, Sharp, Structure Solution
CNS 1.1, Coot, CCP4 Structure Refinement
Software
Software Name Purpose
CCP4 refinement
Coot refinement
CNS version: 1.1 refinement
Sharp model building
ShelxD model building
CBASS data collection