3GVF

1.7 Angstrom crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei bound with phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EIY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.3289100 MM NA/K PHOSPHATE, 50% PEG 200, PH 6.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties
Matthews coefficientSolvent content
3.7467.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.212α = 90
b = 100.212β = 90
c = 110.667γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2008-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0APS23-ID-D

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
11.755098.20.09814.21433131
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)
11.751.811000.63214.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3EIY1.75503303616890.1750.1750.185RANDOM14.99
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]
0.550.270.55-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.198
r_dihedral_angle_4_deg17.205
r_dihedral_angle_3_deg12.379
r_dihedral_angle_1_deg5.222
r_scangle_it2.595
r_scbond_it1.556
r_angle_refined_deg1.146
r_mcangle_it0.872
r_angle_other_deg0.804
r_mcbond_it0.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.198
r_dihedral_angle_4_deg17.205
r_dihedral_angle_3_deg12.379
r_dihedral_angle_1_deg5.222
r_scangle_it2.595
r_scbond_it1.556
r_angle_refined_deg1.146
r_mcangle_it0.872
r_angle_other_deg0.804
r_mcbond_it0.446
r_mcbond_other0.105
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1325
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms34

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling