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Structure of a putative inorganic pyrophosphatase from the oil-degrading bacterium Oleispira antarctica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EIP Swiss-Modeller model based on coordinates from 2EIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 2M Ammonium Sulfate, 0.1M Bis-Tris, cryoprotected in Paratone-N oil, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.23 44.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.666 α = 90 b = 110.666 β = 90 c = 74.324 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2009-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.63 32.56 99.1 0.056 38.72 10.5 21906 21698 -3 21.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.69 92.4 6.3 10 2008
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Swiss-Modeller model based on coordinates from 2EIP 1.63 32.56 20583 1111 99.66 0.17575 0.17387 0.1792 0.21227 0.2172 RANDOM 20.29
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 5.875 r_dihedral_angle_4_deg 5.429 r_scangle_it 3.878 r_scbond_it 2.532 r_mcangle_it 1.756 r_angle_refined_deg 1.527 r_mcbond_it 1.027 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 5.875 r_dihedral_angle_4_deg 5.429 r_scangle_it 3.878 r_scbond_it 2.532 r_mcangle_it 1.756 r_angle_refined_deg 1.527 r_mcbond_it 1.027 r_nbtor_refined 0.311 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.113 r_metal_ion_refined 0.101 r_symmetry_hbond_refined 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 Atoms Number Protein Atoms 1325 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling