X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 20% PEG MME 2000, 0.1M Tris pH 8.5, 0.01M nickel chloride hexahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.58 α = 90
b = 70.58 β = 90
c = 50.14 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2010-05-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 PHOTON FACTORY AR-NW12A

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 50 99.4 0.073 -- -- 4.6 -- 22811 0.0 0.0 16.6
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 1.55 99.5 0.397 -- 3.96 4.5 --

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 1.5 26.1 -- 0.0 21979 21979 2184 96.0 0.184 0.181 0.181 0.205 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 3094 347 3094 0.217 0.259 0.014 90.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 17.4
Anisotropic B[1][1] 0.72
Anisotropic B[1][2] 1.21
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.44
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.88
c_dihedral_angle_d 27.0
c_angle_deg 1.5
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.15
Luzzati Sigma A (Observed) 0.11
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.18
Luzzati Sigma A (R-Free Set) 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1091
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 180

Software

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