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Complex of 6-hydroxy-L-nicotine oxidase with inhibitor bound at active site and turnover product at exit cavity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K7M PDB code 3K7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20mM Sodium phosphate; 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.87 68.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.677 α = 90 b = 163.677 β = 90 c = 163.677 γ = 90
Symmetry Space Group P 4 3 2
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 MAR CCD 165 mm mirror 2003-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 2.15 20 99.4 0.1 14 4.5 41095 40984 2 33.98
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 2.15 2.19 99.6 0.718 2 4.5 2023
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 code 3K7M 2.15 14.4 39048 38825 2054 99.43 0.16648 0.16422 0.1802 0.21043 0.2171 RANDOM 33.234
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 38.333 r_dihedral_angle_4_deg 19.168 r_dihedral_angle_3_deg 15.776 r_dihedral_angle_1_deg 7.309 r_scangle_it 5.785 r_scbond_it 3.825 r_mcangle_it 2.377 r_angle_refined_deg 2.269 r_mcbond_it 1.531 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.333 r_dihedral_angle_4_deg 19.168 r_dihedral_angle_3_deg 15.776 r_dihedral_angle_1_deg 7.309 r_scangle_it 5.785 r_scbond_it 3.825 r_mcangle_it 2.377 r_angle_refined_deg 2.269 r_mcbond_it 1.531 r_nbtor_refined 0.326 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.228 r_symmetry_hbond_refined 0.227 r_symmetry_vdw_refined 0.222 r_chiral_restr 0.187 r_bond_refined_d 0.029 r_gen_planes_refined 0.012 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_refined 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 3272 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 123
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling