X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 21.0
Details PEG 8000, Zinc Acetate, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.27 α = 90
b = 87.27 β = 90
c = 164.1 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 130
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS -- 2000-04-20
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 0.9786, 0.9788, 0.9390, 1.078 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
2.2 40 74.0 0.058 -- -- 16.6 48740 35024 1.0 3.0 41.6
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)
2.3 2.4 71.8 0.25 -- -- 16.4 2766

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
MAD 2.3 100.0 1.0 1.0 35024 28907 1444 88.0 -- -- 0.21 0.247 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 2.3 2.4 -- 123 2766 0.349 0.373 0.034 71.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 49.3
Anisotropic B[1][1] 0.17
Anisotropic B[1][2] -0.48
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.33
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.31
x_dihedral_angle_d 25.3
x_angle_deg 1.5
x_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.41
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2638
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 176

Software

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