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Crystal structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii in I213 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 22% PEG3350, 100mM sodium citrate, Bis-Tris propan pH6.5
Crystal Properties Matthews coefficient Solvent content 4.95 75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.853 α = 90 b = 180.853 β = 90 c = 180.853 γ = 90
Symmetry Space Group I 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 PIXEL DECTRIS PILATUS 6M mirrors 2012-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97 Diamond I03
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 2.3 50 0.996 0.101 13.6 5 43479 43.3
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 2.3 2.38 99.2 0.73 2.2 4.9
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 3ZIY 2.3 50 41187 2183 99.41 0.13547 0.13407 0.1431 0.16166 0.1664 RANDOM 46.403
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_2_deg 37.013 r_dihedral_angle_4_deg 21.449 r_dihedral_angle_3_deg 12.914 r_long_range_B_refined 8.104 r_long_range_B_other 7.989 r_dihedral_angle_1_deg 6.976 r_scangle_other 6.455 r_scbond_other 4.408 r_scbond_it 4.407 r_mcangle_other 4.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.013 r_dihedral_angle_4_deg 21.449 r_dihedral_angle_3_deg 12.914 r_long_range_B_refined 8.104 r_long_range_B_other 7.989 r_dihedral_angle_1_deg 6.976 r_scangle_other 6.455 r_scbond_other 4.408 r_scbond_it 4.407 r_mcangle_other 4.382 r_mcangle_it 4.38 r_mcbond_it 3.1 r_mcbond_other 3.087 r_angle_refined_deg 1.67 r_angle_other_deg 0.997 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3435 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing