X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.7
Details pH 5.7

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.23 α = 90
b = 84.23 β = 90
c = 40.96 γ = 120
Symmetry
Space Group P 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 283
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU MIRROR 1996-11
Diffraction Radiation
Monochromator Protocol
SI(111) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B -- PHOTON FACTORY BL-6B

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
1.54 20 90.9 0.036 -- -- 2.4 -- 43724 -- 6.0 13.8
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)
1.54 1.62 81.9 0.276 -- 2.4 1.9 --

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
MOLECULAR REPLACEMENT 1.54 20.0 -- 0.0 -- 43723 1759 90.9 -- 0.164 0.164 0.192 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 1.54 1.61 -- 205 4713 0.275 0.31 0.022 81.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 14.8
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 4.53
x_scbond_it 2.75
x_mcangle_it 1.6
x_mcbond_it 1.08
x_improper_angle_d 0.82
x_bond_d 0.008
x_angle_deg 1.4
x_dihedral_angle_d 27.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.14
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.16
Luzzati Sigma A (R-Free Set) 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2655
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 248

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 Data Reduction (data scaling)
X-PLOR 3.851 Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
X-PLOR version: 3.851 model building