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Atomic Resolution Structure of Resting State of the Achromobacter cycloclastes Cu Nitrite Reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NIF PDB ENTRY 1NIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 1.6M AMMONIUM SULPHATE, 100MM SODIUM ACETATE, PH 4.75
Crystal Properties Matthews coefficient Solvent content 2 36.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.414 α = 90 b = 95.414 β = 90 c = 95.414 γ = 90
Symmetry Space Group P 21 3
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 2005-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 SRS PX10.1
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 0.9 19.5 98.1 0.06 24 5.2 208276 5.4
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 0.9 0.92 85.9 0.55 2 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NIF 0.9 19.48 195768 8169 96.1 0.118 0.117 0.134 0.1396 RANDOM 7
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 21.067 r_dihedral_angle_3_deg 12.5 r_dihedral_angle_1_deg 7.916 r_scangle_it 3.697 r_scbond_it 3.025 r_angle_other_deg 2.332 r_mcangle_it 2.213 r_angle_refined_deg 2.167 r_mcbond_it 1.819 r_symmetry_vdw_refined 0.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 21.067 r_dihedral_angle_3_deg 12.5 r_dihedral_angle_1_deg 7.916 r_scangle_it 3.697 r_scbond_it 3.025 r_angle_other_deg 2.332 r_mcangle_it 2.213 r_angle_refined_deg 2.167 r_mcbond_it 1.819 r_symmetry_vdw_refined 0.355 r_xyhbond_nbd_refined 0.297 r_nbd_refined 0.286 r_symmetry_vdw_other 0.286 r_symmetry_hbond_refined 0.263 r_nbd_other 0.217 r_chiral_restr 0.135 r_nbtor_other 0.103 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_nbtor_refined 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 2581 Nucleic Acid Atoms Solvent Atoms 633 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing