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Complex of 6-hydroxy-L-nicotine oxidase with final ketone product formed during catalytic turnover
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 3.83 67.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.051 α = 90 b = 163.051 β = 90 c = 163.051 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 2.1 20 100 0.116 20 8.5 43679 43679 2 31.4
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 2.1 2.14 100 0.704 2.5 8.5 2137
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 2.1 12.22 41274 41266 2184 99.98 0.16077 0.15855 0.1824 0.20372 0.2141 RANDOM 31.533
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 40.207 r_dihedral_angle_4_deg 19.739 r_dihedral_angle_3_deg 16.248 r_scangle_it 6.741 r_dihedral_angle_1_deg 6.63 r_scbond_it 4.484 r_mcangle_it 2.74 r_angle_refined_deg 2.369 r_mcbond_it 1.846 r_symmetry_hbond_refined 0.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.207 r_dihedral_angle_4_deg 19.739 r_dihedral_angle_3_deg 16.248 r_scangle_it 6.741 r_dihedral_angle_1_deg 6.63 r_scbond_it 4.484 r_mcangle_it 2.74 r_angle_refined_deg 2.369 r_mcbond_it 1.846 r_symmetry_hbond_refined 0.519 r_symmetry_vdw_refined 0.392 r_nbtor_refined 0.327 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.218 r_chiral_restr 0.208 r_bond_refined_d 0.031 r_gen_planes_refined 0.014 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 3270 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 123
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling