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Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C0U PDB ENTRY 2C0U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 25%(W/V) PEG 4000, 35% (V/V) GLYCEROL, 200 MM SODIUM CACODYLATE TRIHYDRATE PH 7.5, 1 MM SPERMINE TETRAHYDROCHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.58 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.393 α = 90 b = 103.393 β = 90 c = 485.134 γ = 120
Symmetry Space Group P 32 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 ADSC CCD 2003-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
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 2.07 50 97.8 0.14 12.6 1.64 180533 3
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 2.07 2.15 81.9 0.269 3 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 ENTRY 2C0U 2.07 50 171484 9048 97.8 0.19 0.188 0.1994 0.225 0.2359 RANDOM 24.66
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] 0.68 0.34 0.68 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.422 r_scangle_it 3.13 r_scbond_it 1.874 r_angle_refined_deg 1.394 r_mcangle_it 1.11 r_angle_other_deg 0.992 r_mcbond_it 0.575 r_symmetry_vdw_other 0.254 r_nbd_other 0.244 r_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.422 r_scangle_it 3.13 r_scbond_it 1.874 r_angle_refined_deg 1.394 r_mcangle_it 1.11 r_angle_other_deg 0.992 r_mcbond_it 0.575 r_symmetry_vdw_other 0.254 r_nbd_other 0.244 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.201 r_symmetry_hbond_refined 0.18 r_symmetry_vdw_refined 0.156 r_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19842 Nucleic Acid Atoms Solvent Atoms 1117 Heterogen Atoms 512
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing