X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details PEG 1500, Ammonium fluoride, urea, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.29 α = 90
b = 78.79 β = 93.37
c = 78.8 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 V -- 2006-07-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU -- SPRING-8 BL41XU

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 50 100.0 -- -- -- -- -- 75469 -- -- 13.9
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 1.76 100.0 -- -- -- -- --

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 45.75 -- 0.0 -- 73953 3755 97.8 -- 0.17 0.17 0.195 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 -- 630 11206 0.184 0.214 0.009 94.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 15.9
Anisotropic B[1][1] 1.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.2
Anisotropic B[2][2] -1.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 5.35
c_scbond_it 3.98
c_mcangle_it 3.14
c_mcbond_it 2.51
c_improper_angle_d 0.79
c_bond_d 0.005
c_angle_deg 1.3
c_dihedral_angle_d 22.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.16
Luzzati Sigma A (Observed) 0.05
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.19
Luzzati Sigma A (R-Free Set) 0.1
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5942
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 719

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
AMoRE Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
AMoRE model building
HKL-2000 data collection