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Pyruvate oxidase variant F479W in complex with reaction intermediate 2-lactyl-thiamin diphosphate
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 hanging drop 5.7 280 ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.9 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.133 α = 90 b = 154.462 β = 90 c = 165.656 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 IMAGE PLATE MAR scanner 345 mm plate 2005-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.97 24.96 98.2 0.107 11.49 4.5 105614 105590 2 3.7 12.8
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 1.97 2 0.871 87.1 0.275 3.5 3.7
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 (All) 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 1.963 24.96 2 105614 105590 2105 97.964 0.149 0.149 0.1486 0.1518 0.1722 0.1739 RANDOM 13.078
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] 1.953 -1.008 -0.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.135 r_dihedral_angle_4_deg 19.193 r_dihedral_angle_3_deg 13.47 r_dihedral_angle_1_deg 6.155 r_scangle_it 3.715 r_scbond_it 2.22 r_angle_refined_deg 1.463 r_mcangle_it 1.153 r_mcbond_it 0.611 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.135 r_dihedral_angle_4_deg 19.193 r_dihedral_angle_3_deg 13.47 r_dihedral_angle_1_deg 6.155 r_scangle_it 3.715 r_scbond_it 2.22 r_angle_refined_deg 1.463 r_mcangle_it 1.153 r_mcbond_it 0.611 r_nbtor_refined 0.301 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9046 Nucleic Acid Atoms Solvent Atoms 993 Heterogen Atoms 186
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing