X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Details PROTEIN WAS CRYSTALLIZED FROM SOLUTIONS CONTAINING 10 MG/ML PROTEIN, 4 MM TRIS BUFFER (PH7.5), AND 16% PEG 4000 (W/V), EQUILIBRATED AGAINST 12% PEG 4000 BY VAPOR DIFFUSION AT ROOM TEMPERATURE., vapor diffusion

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.66 α = 90
b = 27.75 β = 102.2
c = 41.79 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 285
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU COLLIMATORS 1994-01
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
1.7 15 81.38 0.042 -- -- -- -- 7813 -- 2.0 25.8
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)
1.7 1.78 58.8 -- -- -- -- --

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
DIFFERENCE FOURIERS 1.7 8.0 -- 2.0 -- 7813 829 81.4 -- 0.217 0.217 0.312 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 1.7 1.78 -- 81 617 0.3605 0.3354 0.037 58.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 36.4
Anisotropic B[1][1] 0.6917
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.5535
Anisotropic B[2][2] -1.6457
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.954
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 7.88
x_scbond_it 5.29
x_mcangle_it 5.46
x_mcbond_it 3.57
x_improper_angle_d 1.58
x_bond_d 0.017
x_angle_deg 3.28
x_dihedral_angle_d 27.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Resolution Cutoff (Low) 8.0
Luzzati ESD (R-Free Set) 0.32
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 673
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 50

Software

Computing
Computing Package Purpose
R-AXIS IIC Data Reduction (intensity integration)
R-AXIS II Data Reduction (data scaling)
X-PLOR Structure Solution
X-PLOR Structure Refinement
Software
Software Name Purpose
X-PLOR refinement
X-PLOR model building