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Crystal structure of apo-form 6-hydroxy-L-nicotine oxidase, crystal form P3121
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 7.5 289 0.1M Hepes, 1.5M lithium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.7 73.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.957 α = 90 b = 122.957 β = 90 c = 199.918 γ = 120
Symmetry Space Group P 31 2 1
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 mirrors 2002-12-12 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) 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 2.85 20 99.2 0.078 0.078 25.3 7.5 41415 41084 2 72.9
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) 2.85 2.9 100 0.75 0.75 2 7.5 2038
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 2.85 16.6 39197 38462 2035 98.14 0.27776 0.27549 0.3167 0.32118 0.3184 RANDOM 72.942
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] 3.72 1.86 3.72 -5.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.675 r_dihedral_angle_3_deg 18.815 r_dihedral_angle_4_deg 17.515 r_dihedral_angle_1_deg 7.599 r_scangle_it 4.256 r_scbond_it 2.467 r_mcangle_it 1.853 r_angle_refined_deg 1.781 r_mcbond_it 1.021 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.675 r_dihedral_angle_3_deg 18.815 r_dihedral_angle_4_deg 17.515 r_dihedral_angle_1_deg 7.599 r_scangle_it 4.256 r_scbond_it 2.467 r_mcangle_it 1.853 r_angle_refined_deg 1.781 r_mcbond_it 1.021 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.294 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.103 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6540 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 192
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling