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Complex of dithionite-reduced 6-hydroxy-L-nicotine oxidase with substrate bound at active site and inhibitor at exit cavity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K7M PDB ENTRY 3K7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 20mM Sodium phosphate, 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.88 68.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.771 α = 90 b = 163.771 β = 90 c = 163.771 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 2003-03-21 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 1.95 20 99.6 0.1 15 5 55164 54943 2 25.95
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 1.95 1.97 96 0.702 2 4.5 2733
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 Molrep THROUGHOUT PDB ENTRY 3K7M 1.95 14.4 54943 51749 2766 99.58 0.16901 0.16715 0.1886 0.20385 0.215 RANDOM 27.643
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 37.188 r_dihedral_angle_4_deg 18.4 r_dihedral_angle_3_deg 15.573 r_dihedral_angle_1_deg 7.072 r_scangle_it 6.434 r_scbond_it 4.382 r_mcangle_it 2.606 r_angle_refined_deg 2.542 r_mcbond_it 1.764 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.188 r_dihedral_angle_4_deg 18.4 r_dihedral_angle_3_deg 15.573 r_dihedral_angle_1_deg 7.072 r_scangle_it 6.434 r_scbond_it 4.382 r_mcangle_it 2.606 r_angle_refined_deg 2.542 r_mcbond_it 1.764 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.239 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.23 r_chiral_restr 0.226 r_xyhbond_nbd_refined 0.224 r_bond_refined_d 0.033 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3292 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 122
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling