X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details Na/Cacodylate, NaCl, MgSO4, PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.09 α = 90
b = 105.09 β = 90
c = 70.63 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 RIGAKU JUPITER 210 -- 2004-03-04
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.9791, 0.9794, 0.9840 SPRING-8 BL26B1

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
2.4 50 99.3 -- 0.09 -- -- -- 17400 -- -- 13.2
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)
2.4 2.44 96.5 -- 0.411 -- -- --

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
MAD 2.4 42.16 -- 0.0 -- 17347 1726 99.5 -- 0.2 0.2 0.27 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 2.4 2.55 -- 285 2494 0.37 0.409 0.024 95.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 45.7
Anisotropic B[1][1] -5.12
Anisotropic B[1][2] 4.72
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.24
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 11.53
c_scbond_it 9.35
c_mcangle_it 7.92
c_mcbond_it 5.71
c_improper_angle_d 1.88
c_dihedral_angle_d 24.0
c_angle_deg 1.6
c_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.55
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.39
Luzzati Sigma A (R-Free Set) 0.66
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2095
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 143

Software

Computing
Computing Package Purpose
DENZO Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
SOLVE model building
DENZO data collection