X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 291.0
Details THE CRYSTAL WAS OBTAINED IN PRESENCE OF NAPTS WITH A FINAL PROTEIN CONCENTRATION OF 40.5 MG/ML IN HANGING DROPS USING VAPOR DIFFUSION METHOD. THE EQUILIBRATION AT 291K WAS DONE AGAINST A RESERVOIR SOLUTION CONTAINING 90 MM NAPTS, 50 MM SODIUM ACETATE ADJUSTED AT PH 4.5., vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.06 α = 90
b = 79.06 β = 90
c = 37.97 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II -- 1994-04-01
Diffraction Radiation
Monochromator Protocol
-- MONOCHROMATIC
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
1.85 13.5 97.5 -- 0.049 -- 6.6 -- 10462 -- 0.0 21.4
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)
1.85 1.9 85.8 -- 0.135 4.5 4.1 --

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
OTHER 1.84 14.0 -- 0.0 -- 10461 1082 96.1 -- -- 0.202 0.241 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 1.84 1.92 -- 104 1067 0.332 0.354 -- 79.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 18.7
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 4.72
x_scbond_it 2.94
x_mcangle_it 2.39
x_mcbond_it 1.52
x_improper_angle_d 1.15
x_bond_d 0.006
x_angle_deg 1.33
x_dihedral_angle_d 23.22
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 86

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 Data Reduction (data scaling)
CCP4 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
CCP4 model building
CCP4 data reduction
MOSFLM data collection