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 10MG/ML PROTEIN, 4 MM TRIS BUFFER (PH7.5), AND 16% PEG 4000 (W/V), EQUILIBRATED AGAINST 12% PEG4000 BY VAPOR DIFFUSION AT ROOM TEMPERATURE., vapor diffusion

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.01 α = 90
b = 28.03 β = 103.1
c = 42.4 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 1995-01
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
2 15 92.9 0.078 -- -- -- -- 5539 -- 2.0 27.6
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)
2.0 2.2 86.3 -- -- -- -- --

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 2.0 8.0 -- 2.0 -- 5539 611 92.9 -- 0.223 0.223 0.326 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 2.0 2.09 -- 65 563 0.364 0.338 0.042 86.38
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.7
Anisotropic B[1][1] -2.92
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.05
Anisotropic B[2][2] -4.84
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.76
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 8.32
x_scbond_it 4.83
x_mcangle_it 5.83
x_mcbond_it 3.62
x_improper_angle_d 1.65
x_bond_d 0.019
x_angle_deg 3.4
x_dihedral_angle_d 27.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Resolution Cutoff (Low) 8.0
Luzzati ESD (R-Free Set) 0.35
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 675
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 48

Software

Computing
Computing Package Purpose
R-AXIS IIC Data Reduction (intensity integration)
R-AXIS II Data Reduction (data scaling)
X-PLOR 3.1 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR version: 3.1 model building