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Pyruvate Oxidase variant V265A from Lactobacillus plantarum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1POW pdb entry 1POW
Crystallization Crystal Properties Matthews coefficient Solvent content 2.8 56.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.66 α = 90 b = 155.78 β = 92.92 c = 100.75 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH 2003-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8123 EMBL/DESY, HAMBURG X13
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 2.2 27.3 0.062 20.6 147394
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 1POW 2.2 27.3 147399 139647 7369 99.69 0.18068 0.17763 0.1789 0.23794 0.2385 RANDOM 46.443
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] 0.37 -0.11 2.38 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.755 r_dihedral_angle_4_deg 19.623 r_dihedral_angle_3_deg 17.462 r_dihedral_angle_1_deg 7.015 r_scangle_it 4.428 r_scbond_it 2.715 r_mcangle_it 1.788 r_angle_refined_deg 1.677 r_mcbond_it 0.971 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.755 r_dihedral_angle_4_deg 19.623 r_dihedral_angle_3_deg 17.462 r_dihedral_angle_1_deg 7.015 r_scangle_it 4.428 r_scbond_it 2.715 r_mcangle_it 1.788 r_angle_refined_deg 1.677 r_mcbond_it 0.971 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.254 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.12 r_metal_ion_refined 0.062 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 17318 Nucleic Acid Atoms Solvent Atoms 1848 Heterogen Atoms 238
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing