3OS4

The Crystal Structure of Nicotinate Phosphoribosyltransferase from Yersinia pestis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52890.2M magnesium chloride hexahydrate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0840.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.394α = 81.95
b = 50.681β = 83.39
c = 87.184γ = 71.95
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2010-08-09MSAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97926APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.65093.40.05815.82.6936459364515.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.6360.50.3463.62.43042

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.60133.9299191091910200091.60.1630.1630.1620.193random22.8
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-2.83681.12060.28220.9932-3.10741.8435
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.628
f_angle_d1.315
f_chiral_restr0.088
f_bond_d0.011
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6161
Nucleic Acid Atoms
Solvent Atoms870
Heterogen Atoms71

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
RESOLVEmodel building
BUCCANEERmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RESOLVEphasing
BUCCANEERphasing