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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 6.5 0.1M MES, PH 6.5, 7.5% PEG 8000 A COCRYSTALLISATION WITH 10MM OF KCLO4 (PERCHLORATE) 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 -80C.
Crystal Properties Matthews coefficient Solvent content 2.42 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.566 α = 90 b = 106.566 β = 90 c = 135.479 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 2004-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.91 46.13 93.5 0.114 10 7 454081 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 1.91 2.01 60.4 1.33 0.8 2.6
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 1.99 92.45 57324 2410 97.1 0.185 0.182 0.1931 0.246 0.2513 RANDOM 19.55
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] -1.33 -0.67 -1.33 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.345 r_dihedral_angle_4_deg 22.004 r_dihedral_angle_3_deg 17.287 r_dihedral_angle_1_deg 6.432 r_scangle_it 2.617 r_scbond_it 1.7 r_angle_refined_deg 1.698 r_mcangle_it 0.941 r_mcbond_it 0.589 r_symmetry_hbond_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.345 r_dihedral_angle_4_deg 22.004 r_dihedral_angle_3_deg 17.287 r_dihedral_angle_1_deg 6.432 r_scangle_it 2.617 r_scbond_it 1.7 r_angle_refined_deg 1.698 r_mcangle_it 0.941 r_mcbond_it 0.589 r_symmetry_hbond_refined 0.314 r_nbtor_refined 0.308 r_xyhbond_nbd_refined 0.239 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 5627 Nucleic Acid Atoms Solvent Atoms 757 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling