X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details 100MM-MES BUFFER AT PH 7.0 USING PEG4K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.69 α = 90
b = 81.13 β = 90
c = 85.79 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV MIRROR/MONOCHROMATOR 1998-08-01
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 -- SPRING-8 BL44B2

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
1.7 100 97.8 0.068 -- -- 5.8 -- 42130 -- 0.0 15.2
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)
1.7 1.76 93.0 0.32 -- -- -- --

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 1.7 50.0 -- 0.0 -- 41680 2130 97.6 -- -- 0.197 0.25 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 1.7 1.81 -- 309 6204 0.276 0.297 0.017 92.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 16.4
RMS Deviations
Key Refinement Restraint Deviation
x_scbond_it 2.28
x_mcbond_it 1.21
x_mcangle_it 1.79
x_scangle_it 3.41
x_bond_d 0.006
x_improper_angle_d 0.78
x_angle_deg 1.2
x_dihedral_angle_d 23.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3100
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 337

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.851 Structure Solution
X-PLOR 3.8 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.8 refinement
X-PLOR version: 3.851 model building