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A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NAP PDB ENTRY 2NAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 COCRYSTALLISATION WITH 200MM OF NO3 (NITRATE) IN 200MM OF DDNAPA (IE PROTEIN) WHICH HAD BEEN REDUCED BY DITHIONITE IN ANAEROBIC CONDITIONS AND THEN AIR REOXIDISED BEFORE SETTTING UP FOR CRYSTALLISATIONS STRAIGHT AFTER THAWING FROM 193K. SAMPLE WAS DIALYSED AND CONCENTRATED BEFORE CRYSTALLISING IN 0.1M MES PH 6.0, 7.5% PEG 8000. CRYSTAL WAS SOAKED WITH 10MM NANO3 CONTAINING CRYOBUFFER.
Crystal Properties Matthews coefficient Solvent content 2.29 52.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.212 α = 90 b = 105.212 β = 90 c = 130.685 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 ADSC CCD 2004-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.43 53 99 0.27 6.3 4.8 31747 1
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 2.43 2.56 93.6 1.14 1 3.7
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 2NAP 2.44 91.29 30226 1258 99.4 0.159 0.155 0.1585 0.248 0.2487 RANDOM 25.75
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] -0.8 -0.4 -0.8 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.959 r_dihedral_angle_4_deg 18.85 r_dihedral_angle_3_deg 17.332 r_dihedral_angle_1_deg 6.985 r_scangle_it 2.635 r_scbond_it 1.672 r_angle_refined_deg 1.604 r_mcangle_it 0.968 r_mcbond_it 0.56 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.959 r_dihedral_angle_4_deg 18.85 r_dihedral_angle_3_deg 17.332 r_dihedral_angle_1_deg 6.985 r_scangle_it 2.635 r_scbond_it 1.672 r_angle_refined_deg 1.604 r_mcangle_it 0.968 r_mcbond_it 0.56 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.23 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.211 r_symmetry_vdw_refined 0.176 r_chiral_restr 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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_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 5622 Nucleic Acid Atoms Solvent Atoms 752 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement MOLREP phasing