X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.3
Details PROTEIN WAS CRYSTALLIZED FROM 0.1M SODIUM CITRATE PH 5.3, 15% V/V 2-PROPANOL AND 20% W/ V PEG 4000.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.01 α = 90
b = 78.8 β = 90
c = 82.31 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH TOROIDAL MIRROR 1995-05-03
Diffraction Radiation
Monochromator Protocol
SI(111) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 -- EMBL/DESY, HAMBURG X31

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
2.3 20 98.8 -- 0.09 -- 4.9 -- 21455 -- -- 28.1
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 2.34 93.5 -- 0.297 3.4 2.9 --

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
MULTIPLE ISOMORPHOUS REPLACEMENT 2.3 20.0 -- 2.0 -- 20814 1040 95.8 -- 0.1627 0.1627 0.213 RANDOM AND UNIFORM DISTRIBUTION
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 2.38 -- 103 1863 0.23 0.269 0.026 92.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 25.9
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 4.0
x_scbond_it 2.9
x_mcangle_it 3.4
x_mcbond_it 2.4
x_improper_angle_d 1.27
x_bond_d 0.009
x_angle_deg 1.7
x_dihedral_angle_d 21.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3672
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 118

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK 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