X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Temperature 277.0
Details Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 100mM HEPES (pH 7.5) and 500mM magnesium Formate dihydrate, microbatch, under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.76 α = 90
b = 110.4 β = 90
c = 107.96 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD mirrors 2009-05-28
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97945 SSRL BL9-2

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 0.082 0.058 -- 7.4 63196 62970 0.0 0.0 15.7
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)
2.2 2.28 98.9 0.483 0.392 2.9 5.6 6275

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 19.7 2.0 2.0 63116 54091 2722 85.7 0.226 0.225 0.224 0.254 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 3612 194 3418 0.231 0.262 0.019 57.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 41.1
Anisotropic B[1][1] -7.99
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.89
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.1
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 24.9
c_improper_angle_d 0.79
c_angle_deg 1.2
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.17
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2898
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 131

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.00
MAR345dtb data collection
DENZO data reduction
SCALEPACK data scaling
SHELX phasing version: then SOLVE/RESOLVE
CNS refinement version: 1.2 & XtalView