2GTA

Crystal Structure of the putative pyrophosphatase YPJD from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR428.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729116% PEG 3350, 0.25 M Sodium Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.0259.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.747α = 90
b = 79.694β = 90
c = 119.568γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97900NSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.93099.50.09512.12487699.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.93.0299.80.31813.32813

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.929.8912383797880.10.2250.2250.263RANDOM53.8
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]
-7.446.26-38.86
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.5
c_angle_deg1.3
c_improper_angle_d0.73
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.5
c_angle_deg1.3
c_improper_angle_d0.73
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2938
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms4

Software

Software
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data scaling
SHELXDphasing
SHELXEmodel building