X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 295.0
Details 16% PEG 8000, 100 mM Tris, 10 mM DTT, pH 8.0, vapor diffusion, hanging drop, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.85 α = 90
b = 49.53 β = 105.03
c = 70 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-02-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 8-BM 0.9795 APS 8-BM

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
2.24 50 95.1 0.105 0.105 -- 3.9 14386 13927 0.0 0.0 20.8
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)
2.24 2.32 99.4 0.317 0.317 4.26 4.0 1485

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 2.24 19.98 0.0 0.0 14386 13927 711 92.0 0.227 0.227 0.227 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 2.24 2.38 1485 102 2103 0.241 0.308 0.03 88.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 32.29
Anisotropic B[1][1] -6.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.2
Anisotropic B[2][2] 20.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -14.02
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.07
c_mcangle_it 2.33
c_scbond_it 2.15
c_angle_deg 1.3
c_bond_d 0.006
c_scangle_it 3.04
c_dihedral_angle_d 25.3
c_mcbond_it 1.45
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.1
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2415
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 76

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement version: 1.2
PDB_EXTRACT data extraction version: 3.005
ADSC data collection version: Quantum
HKL-2000 data reduction
CNS phasing