X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details Protein: 2-5 mg/ml, 50 mM Tris pH=8.2, 10 mM CaCl2 and 0.5 M NaCl. Reservoir: 0.8-1.0 M Na2-Tartrate, 80 mM Li2SO4 and 0.1 MES pH=6.5, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.41 α = 90
b = 103.9 β = 119.93
c = 70.48 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
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.979 SSRL BL11-1

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
2.7 39.56 98.7 -- -- -- -- 23987 23873 -- -3.7 --
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)
2.7 2.77 99.6 -- -- -- -- --

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
SIRAS 2.7 39.56 -- 0.0 23873 23873 2357 -- -- -- 0.248 0.283 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 2.7 2.87 -- 392 3585 0.336 0.376 0.019 99.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 44.0
Anisotropic B[1][1] -5.13
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.69
Anisotropic B[2][2] -9.96
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 15.09
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_dihedral_angle_d 26.5
c_improper_angle_d 0.83
c_scbond_it 5.31
c_scangle_it 6.9
c_mcbond_it 1.58
c_mcangle_it 2.84
c_angle_deg 1.4
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.45
Luzzati Sigma A (R-Free Set) 0.48
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4050
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 106

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
SOLVE phasing
CNS refinement
CCP4 data scaling version: (SCALA)
CNS phasing