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Crystal structure of inhibitor-bound in active centre 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K7M PDB 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 3.91 68.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.184 α = 90 b = 164.184 β = 90 c = 164.184 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 2009-09-17 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 2.19 20 99.8 0.085 21.5 5.5 39391 39330 2 34.8
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 2.19 2.23 100 0.645 3 5.5 1909
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 3K7M 2.19 14.4 38110 37196 1962 99.7 0.17046 0.16827 0.1806 0.21249 0.2176 RANDOM 30.743
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 38.127 r_dihedral_angle_4_deg 20.117 r_dihedral_angle_3_deg 15.436 r_dihedral_angle_1_deg 6.732 r_scangle_it 5.777 r_scbond_it 4.007 r_angle_refined_deg 2.34 r_mcangle_it 2.333 r_mcbond_it 1.562 r_symmetry_vdw_refined 0.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.127 r_dihedral_angle_4_deg 20.117 r_dihedral_angle_3_deg 15.436 r_dihedral_angle_1_deg 6.732 r_scangle_it 5.777 r_scbond_it 4.007 r_angle_refined_deg 2.34 r_mcangle_it 2.333 r_mcbond_it 1.562 r_symmetry_vdw_refined 0.438 r_symmetry_hbond_refined 0.364 r_nbtor_refined 0.32 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.19 r_bond_refined_d 0.03 r_gen_planes_refined 0.011 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 430 Heterogen Atoms 109
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling