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crystal structure of the Molybdenum-containing nitrate reducing fragment of Pichia angusta assimilatory nitrate reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGP PDB ENTRY 1OGP
Crystallization Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.74 α = 90 b = 76.74 β = 90 c = 306.086 γ = 120
Symmetry Space Group P 61 2 2
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 MARRESEARCH MIRRORS 2003-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
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 2.6 30 99.6 0.09 24.7 8 17438
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 2.6 2.64 99.8 0.44 3.3
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 1OGP 2.6 65.94 17366 880 99.6 0.193 0.19 0.196 0.258 0.2676 RANDOM 46.81
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] 2.454 1.227 2.454 -3.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.908 r_dihedral_angle_4_deg 17.866 r_dihedral_angle_3_deg 16.601 r_dihedral_angle_1_deg 8.406 r_scangle_it 2.474 r_angle_refined_deg 1.901 r_scbond_it 1.65 r_mcangle_it 1.042 r_mcbond_it 0.873 r_angle_other_deg 0.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.908 r_dihedral_angle_4_deg 17.866 r_dihedral_angle_3_deg 16.601 r_dihedral_angle_1_deg 8.406 r_scangle_it 2.474 r_angle_refined_deg 1.901 r_scbond_it 1.65 r_mcangle_it 1.042 r_mcbond_it 0.873 r_angle_other_deg 0.848 r_symmetry_hbond_refined 0.535 r_symmetry_vdw_refined 0.3 r_symmetry_vdw_other 0.258 r_nbd_refined 0.217 r_nbd_other 0.203 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.129 r_nbtor_other 0.092 r_chiral_restr 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3654 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing