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_improper_angle_d 1.88
c_mcbond_it 5.71
c_scbond_it 9.35
c_bond_d 0.01
c_scangle_it 11.53
c_dihedral_angle_d 24.0
c_mcangle_it 7.92
c_angle_deg 1.6
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

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