X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Under Oil
pH 7
Temperature 277.0
Details Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1 Bis-Tris Propane (pH 7) and 1.88M sodium sulfate, Microbatch, under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 203.07 α = 90
b = 203.07 β = 90
c = 101.8 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 mirrors 2002-01-01
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A 0.97870 NSLS X6A

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
3 30 99.9 0.098 0.072 -- 4.9 94054 93958 0.0 0.0 65.4
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)
3.0 3.11 100.0 0.488 0.413 3.6 4.9 9419

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 3.0 19.96 2.0 2.0 93781 81215 7907 86.6 0.188 0.183 0.18 0.219 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 3.0 3.11 5622 602 5622 0.255 0.294 0.012 66.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 50.42
Anisotropic B[1][1] -5.68
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.35
RMS Deviations
Key Refinement Restraint Deviation
BOND LENGTHS 0.009
BOND ANGLES 1.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.4
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.35
Luzzati Sigma A (R-Free Set) 0.49
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9476
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 164

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.100
ADSC data collection version: Quantum
HKL-2000 data reduction
SCALEPACK data scaling
SHELX phasing
SOLVE phasing
RESOLVE phasing
CNS refinement version: 1.2