X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details Na/Cacodylate, MgCl2, PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.5 α = 90
b = 104.5 β = 90
c = 70.85 γ = 120
Symmetry
Space Group P 64

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-06-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 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
1.8 50 98.6 -- -- -- -- -- 40321 -- -- 26.7
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)
1.8 1.83 92.5 -- -- -- -- --

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 1.8 42.05 -- 0.0 -- 40310 4049 98.5 -- 0.19 0.19 0.225 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 1.8 1.91 -- 677 5790 0.346 0.347 0.013 95.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 43.2
Anisotropic B[1][1] -1.7
Anisotropic B[1][2] 2.66
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.7
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.39
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 8.45
c_scbond_it 6.41
c_mcangle_it 5.06
c_mcbond_it 3.95
c_improper_angle_d 1.89
c_dihedral_angle_d 23.6
c_angle_deg 1.6
c_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.35
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2076
Nucleic Acid Atoms 0
Heterogen Atoms 51
Solvent Atoms 224

Software

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