X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.6
Details PROTEIN WAS CRYSTALLIZED FROM 18.0% PEG 4000, 0.2 M SODIUM MALEATE, PH 5.6

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 124.48 α = 90
b = 121.44 β = 90
c = 55.07 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 RIGAKU MIRRORS 1996-03-08
Diffraction Radiation
Monochromator Protocol
NI FILTER --
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
2.5 123 97.2 0.0701 -- -- 3.3 -- 26633 -- 1.0 24.5
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)
2.5 2.8 96.1 0.145 -- 5.2 2.4 --

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 2.5 6.0 -- 2.0 -- 24424 2407 89.3 -- 0.171 0.171 0.245 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 2.5 2.64 -- 346 3256 0.229 0.286 0.015 80.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.4
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 2.72
x_scbond_it 1.71
x_mcangle_it 1.87
x_mcbond_it 1.09
x_improper_angle_d 1.22
x_bond_d 0.006
x_angle_deg 1.21
x_dihedral_angle_d 23.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.33
Luzzati Sigma A (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5941
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 248

Software

Computing
Computing Package Purpose
PROCESS (RIGAKU) Data Reduction (intensity integration)
PROCESS (RIGAKU) 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