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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 10MM OF KCN (CYANIDE) 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. CRYSTALLISING CONDITIONS IN 0.1M MES PH 6.0, 8% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.44 54.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.243 α = 90 b = 106.243 β = 90 c = 134.626 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 2.35 54.31 100 0.01 13.6 6.1 37165 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 2.35 2.48 100 0.72 2.1 6.2
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 2.35 92.06 35628 1500 100 0.167 0.164 0.1588 0.235 0.2273 RANDOM 47.17
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] -2.78 -1.39 -2.78 4.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.026 r_dihedral_angle_4_deg 19.047 r_dihedral_angle_3_deg 17.194 r_dihedral_angle_1_deg 6.663 r_scangle_it 2.507 r_scbond_it 1.681 r_angle_refined_deg 1.568 r_mcangle_it 0.929 r_mcbond_it 0.569 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.026 r_dihedral_angle_4_deg 19.047 r_dihedral_angle_3_deg 17.194 r_dihedral_angle_1_deg 6.663 r_scangle_it 2.507 r_scbond_it 1.681 r_angle_refined_deg 1.568 r_mcangle_it 0.929 r_mcbond_it 0.569 r_nbtor_refined 0.309 r_xyhbond_nbd_refined 0.226 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.159 r_chiral_restr 0.109 r_bond_refined_d 0.013 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 669 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement REFMAC phasing