X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.7
Temperature 290.0
Details PEG 8000, Ammonium Acetate, DTT, Tris-HCl, pH 5.7, VAPOR DIFFUSION, HANGING DROP at 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 170.92 α = 90
b = 170.92 β = 90
c = 69.43 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Mirrors 1999-05-17
Diffraction Radiation
Monochromator Protocol
Ni Filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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
2.2 50 93.8 0.067 -- -- 5.1 58693 55202 -- 0.0 31.8
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)
2.2 2.23 100.0 0.269 -- 2.64 4.98 1953

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 2.2 50.0 -- 2.0 58693 52877 2633 89.7 0.162 0.16 0.16 0.202 FROM PDB ENTRY 1D8D
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 2.2 2.3 5611 285 5326 0.237 0.255 0.015 76.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 34.5
Anisotropic B[1][1] -1.652
Anisotropic B[1][2] 0.294
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.652
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.143
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 5.63
x_scbond_it 3.78
x_mcangle_it 3.18
x_mcbond_it 2.03
x_improper_angle_d 1.32
x_bond_d 0.008
x_angle_deg 1.3
x_dihedral_angle_d 21.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.25
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.26
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5997
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 436

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
X-PLOR model building