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Pyruvate oxidase variant F479W
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1POW pdb entry 1POW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 280 ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.9 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.346 α = 90 b = 154.18 β = 90 c = 165.432 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2005-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 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 2.03 99 29.59 0.107 10.18 3.8 92857 92824 3.7 2 17.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.06 92.95 93.3 0.343 2.83 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2.03 29.59 3.7 92823 92823 1884 94.539 0.156 0.1556 0.158 0.1859 0.1887 RANDOM 16.19
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] 1.631 -0.61 -1.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.038 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_3_deg 13.225 r_dihedral_angle_1_deg 6.054 r_scangle_it 3.348 r_scbond_it 1.997 r_angle_refined_deg 1.352 r_mcangle_it 1.056 r_mcbond_it 0.554 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.038 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_3_deg 13.225 r_dihedral_angle_1_deg 6.054 r_scangle_it 3.348 r_scbond_it 1.997 r_angle_refined_deg 1.352 r_mcangle_it 1.056 r_mcbond_it 0.554 r_nbtor_refined 0.302 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.195 r_symmetry_hbond_refined 0.14 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.09 r_metal_ion_refined 0.018 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9046 Nucleic Acid Atoms Solvent Atoms 965 Heterogen Atoms 172
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing