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Crystal structure of substrate-bound 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 ENTRY 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 3.89 68.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.988 α = 90 b = 162.988 β = 90 c = 162.988 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 130 mm KB-mirror 2001-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 0.782 ESRF ID13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.05 20 100 0.109 0.109 22 11 47039 47039 2 31.38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.05 2.1 100 0.71 0.71 3.3 11 3282
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 2.05 12.22 44283 44208 2343 99.83 0.20398 0.20159 0.2105 0.24967 0.2335 RANDOM 31.389
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 36.28 r_dihedral_angle_4_deg 20.192 r_dihedral_angle_3_deg 14.73 r_dihedral_angle_1_deg 6.8 r_scangle_it 6.425 r_scbond_it 4.292 r_angle_refined_deg 3.007 r_mcangle_it 2.75 r_mcbond_it 1.808 r_nbtor_refined 0.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.28 r_dihedral_angle_4_deg 20.192 r_dihedral_angle_3_deg 14.73 r_dihedral_angle_1_deg 6.8 r_scangle_it 6.425 r_scbond_it 4.292 r_angle_refined_deg 3.007 r_mcangle_it 2.75 r_mcbond_it 1.808 r_nbtor_refined 0.351 r_symmetry_vdw_refined 0.289 r_nbd_refined 0.279 r_symmetry_hbond_refined 0.261 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.201 r_bond_refined_d 0.032 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3323 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 109
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling