3I4Q

Structure of a putative inorganic pyrophosphatase from the oil-degrading bacterium Oleispira antarctica


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52942M Ammonium Sulfate, 0.1M Bis-Tris, cryoprotected in Paratone-N oil, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.2344.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.666α = 90
b = 110.666β = 90
c = 74.324γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2009-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54178

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
11.6332.5699.10.05638.7210.52190621698-321.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.631.6992.46.3102008

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 REPLACEMENTTHROUGHOUTSwiss-Modeller model based on coordinates from 2EIP1.6332.5620583111199.660.175750.173870.21227RANDOM20.29
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.681
r_dihedral_angle_3_deg13.163
r_dihedral_angle_1_deg5.875
r_dihedral_angle_4_deg5.429
r_scangle_it3.878
r_scbond_it2.532
r_mcangle_it1.756
r_angle_refined_deg1.527
r_mcbond_it1.027
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.681
r_dihedral_angle_3_deg13.163
r_dihedral_angle_1_deg5.875
r_dihedral_angle_4_deg5.429
r_scangle_it3.878
r_scbond_it2.532
r_mcangle_it1.756
r_angle_refined_deg1.527
r_mcbond_it1.027
r_nbtor_refined0.311
r_nbd_refined0.213
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.141
r_chiral_restr0.113
r_metal_ion_refined0.101
r_symmetry_hbond_refined0.099
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms174
Heterogen Atoms2

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling