X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details 100 mM Bis-tris (pH 6.0), and 2.7-3.0 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.51 α = 90
b = 92.51 β = 90
c = 78.11 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 MIRRORS --
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A -- NSLS X4A

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
2.8 30 99.8 0.047 -- -- 3.6 -- 9841 -- -- 68.4
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)
2.8 2.9 99.3 0.335 -- 3.197 3.5 --

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
SAD 2.8 29.84 -- 1.0 -- 8690 906 88.6 -- 0.213 0.213 0.248 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 2.8 2.9 -- 64 559 0.298 0.334 0.042 64.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Anisotropic B[1][1] 10.37
Anisotropic B[1][2] 15.82
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -18.96
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.96
c_mcangle_it 2.55
c_bond_d 0.007
c_angle_deg 1.4
c_mcbond_it 1.45
c_dihedral_angle_d 21.5
c_scangle_it 3.02
c_scbond_it 1.88
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.45
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1422
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 47

Software

Software
Software Name Purpose
SnB phasing version: THEN SOLVE/RESOLVE
CNS refinement version: 1.1
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing