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Atomic Resolution Structure of Nitrite -soaked Achromobacter cycloclastes Cu Nitrite Reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BW4 PDB ENTRY 2BW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.75 1.6M AMMONIUM SULPHATE, 10MM SODIUM ACETATE, PH 4.75
Crystal Properties Matthews coefficient Solvent content 2 36.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.224 α = 90 b = 95.224 β = 90 c = 95.224 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 ADSC CCD MIRROR 2005-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 1.1 50 98.2 0.07 18 4.4 113799 9.76
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 1.1 1.12 88.8 0.67 2 3.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BW4 1.1 30 107875 5703 98.1 0.121 0.12 0.1355 0.145 0.1565 RANDOM 11.54
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 17.956 r_dihedral_angle_3_deg 12.799 r_dihedral_angle_1_deg 7.879 r_scangle_it 3.841 r_scbond_it 3.175 r_mcangle_it 2.351 r_angle_refined_deg 1.995 r_mcbond_it 1.989 r_angle_other_deg 1.597 r_symmetry_hbond_refined 0.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 17.956 r_dihedral_angle_3_deg 12.799 r_dihedral_angle_1_deg 7.879 r_scangle_it 3.841 r_scbond_it 3.175 r_mcangle_it 2.351 r_angle_refined_deg 1.995 r_mcbond_it 1.989 r_angle_other_deg 1.597 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.279 r_symmetry_vdw_refined 0.271 r_symmetry_vdw_other 0.264 r_xyhbond_nbd_refined 0.261 r_nbd_other 0.22 r_chiral_restr 0.129 r_nbtor_other 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 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 2582 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing