1WPP

Structure of Streptococcus gordonii inorganic pyrophosphatase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, STREAK SEEDING5.6293sodium citrate, ammonium sulphate, K/Na-tartrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, STREAK SEEDING, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.347.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.08α = 90
b = 148.96β = 90
c = 43.72γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A0.879EMBL/DESY, HAMBURGBW7A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.052097.84018240182-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.197.6

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0519.69381713817120101000.169120.169120.166580.21647RANDOM22.56
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]
1.25-1.350.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.889
r_scangle_it4.093
r_scbond_it2.544
r_angle_refined_deg1.535
r_mcangle_it1.494
r_mcbond_it0.855
r_nbd_refined0.18
r_symmetry_vdw_refined0.18
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.889
r_scangle_it4.093
r_scbond_it2.544
r_angle_refined_deg1.535
r_mcangle_it1.494
r_mcbond_it0.855
r_nbd_refined0.18
r_symmetry_vdw_refined0.18
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.124
r_chiral_restr0.111
r_metal_ion_refined0.111
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4704
Nucleic Acid Atoms
Solvent Atoms536
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
CNSphasing