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: 100mM Bis-Tris Propane (pH 7), 24% (w/v) PEG 20000, and 100mM Lithium sulfate monohydrate., Microbatch, under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.1 α = 90
b = 97.83 β = 90
c = 114.81 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2009-07-07
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 0.97938 SSRL BL7-1

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
2.2 30 99.8 0.113 0.084 -- 6.6 71494 71052 0.0 0.0 8.8
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)
2.2 2.28 99.1 0.437 0.376 3.31 5.3 7096

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 2.2 19.88 2.0 2.0 71425 60712 3014 85.0 0.187 0.186 0.185 0.233 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 2.2 2.28 3994 206 3788 0.197 0.235 0.016 55.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 22.6
Anisotropic B[1][1] -1.88
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.83
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.95
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.006
c_angle_deg 1.2
c_dihedral_angle_d 23.3
c_improper_angle_d 0.82
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.29
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4013
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 374

Software

Software
Software Name Purpose
CNS refinement version: 1.2 & XtalView
PDB_EXTRACT data extraction version: 3.00
ADSC data collection version: Quantum
DENZO data reduction
SCALEPACK data scaling
SnB phasing version: then SOLVE/RESOLVE
REFMAC refinement