X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details PEG6000, MES, sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.65 α = 90
b = 52.59 β = 106.45
c = 47.57 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Bending magnet 2000-01-25
Diffraction Radiation
Monochromator Protocol
fixed-exit double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL40B2 1.0 SPring-8 BL40B2

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
1.5 21.89 96.3 -- -- -- -- 33441 33441 -- -- 13.7
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)
1.5 1.53 90.6 -- -- -- -- --

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 1.5 21.89 -- 0.0 33368 33368 1653 96.0 -- 0.172 0.172 0.202 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 1.5 1.59 -- 257 5078 0.173 0.204 0.013 92.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 14.2
Anisotropic B[1][1] -0.98
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.31
Anisotropic B[2][2] 1.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.8
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 2.0
c_scbond_it 3.26
c_scangle_it 4.28
c_mcbond_it 1.92
c_dihedral_angle_d 23.8
c_improper_angle_d 1.54
c_bond_d 0.022
c_mcangle_it 2.52
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.14
Luzzati Sigma A (Observed) -0.03
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.17
Luzzati Sigma A (R-Free Set) 0.05
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1643
Nucleic Acid Atoms 0
Heterogen Atoms 59
Solvent Atoms 266

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHARP phasing
CNS refinement version: 1.1