X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details PROTEIN WAS CRYSTALLIZED FROM 10% PEG 3350, 3.5 MM CALCIUM CHLORIDE, 10 MM TRIS/HCL, PH 7.5.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.59 α = 90
b = 74.06 β = 90
c = 117.01 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 288
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU COLLIMATOR 1995-10
Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A -- PHOTON FACTORY BL-6A

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
2.5 100 80.4 0.07 -- -- 2.5 -- 19373 -- 2.0 12.2
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 2.61 44.0 0.19 -- 5.0 2.5 --

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
MIR 2.5 7.0 -- 2.0 -- 17162 1676 80.4 -- 0.198 0.198 0.252 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 2.65 -- 174 1563 0.268 0.376 0.027 49.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 15.9
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 4.8
x_scbond_it 3.44
x_mcangle_it 3.42
x_mcbond_it 3.24
x_improper_angle_d 1.21
x_bond_d 0.008
x_angle_deg 1.4
x_dihedral_angle_d 24.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.33
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.36
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3322
Nucleic Acid Atoms 0
Heterogen Atoms 59
Solvent Atoms 146

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE Structure Solution
X-PLOR 3.8 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.8 refinement
MLPHARE model building