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Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase from A. faecalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SNR PDB Entry 1SNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 8-10% PEG 4000, 0.1 M NaOAC, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.552 α = 90 b = 102.428 β = 90 c = 145.744 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH Osmic mirrors 2005-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.85 30 91.5 0.116 4.3 72738
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) 1.85 1.92 100 0.41 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1SNR 1.85 30 1.85 96266 69067 3627 91.52 0.15192 0.15044 0.1526 0.1804 0.1517 RANDOM 16.96
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] 1.07 -0.73 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.615 r_dihedral_angle_4_deg 19.147 r_dihedral_angle_3_deg 11.858 r_dihedral_angle_1_deg 6.923 r_scangle_it 2.613 r_scbond_it 1.699 r_angle_refined_deg 1.264 r_mcangle_it 0.978 r_mcbond_it 0.629 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.615 r_dihedral_angle_4_deg 19.147 r_dihedral_angle_3_deg 11.858 r_dihedral_angle_1_deg 6.923 r_scangle_it 2.613 r_scbond_it 1.699 r_angle_refined_deg 1.264 r_mcangle_it 0.978 r_mcbond_it 0.629 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.089 r_metal_ion_refined 0.044 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7739 Nucleic Acid Atoms Solvent Atoms 1106 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing