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Crystal structure of T2D three-domain heme-Cu nitrite reductase from Ralstonia pickettii
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 7.5 298 Bis-Tris propane, 01M citrate, 22% P3350 MME
Crystal Properties Matthews coefficient Solvent content 2.75 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.23 α = 90 b = 128.23 β = 90 c = 86.11 γ = 120
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 2012-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.2 46.66 98.9 0.102 0.067 0.993 3.3 26499 40.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 90.9 0.535 0.43 0.559 2.1 2.6
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 2.2 46.66 25151 1343 98.88 0.13807 0.13608 0.1436 0.17538 0.1777 RANDOM 30.748
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] -0.38 -0.19 -0.38 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.368 r_dihedral_angle_4_deg 17.364 r_dihedral_angle_3_deg 14.093 r_long_range_B_refined 7.628 r_long_range_B_other 7.275 r_dihedral_angle_1_deg 6.736 r_scangle_other 4.338 r_scbond_other 2.636 r_scbond_it 2.635 r_mcangle_it 2.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.368 r_dihedral_angle_4_deg 17.364 r_dihedral_angle_3_deg 14.093 r_long_range_B_refined 7.628 r_long_range_B_other 7.275 r_dihedral_angle_1_deg 6.736 r_scangle_other 4.338 r_scbond_other 2.636 r_scbond_it 2.635 r_mcangle_it 2.195 r_mcangle_other 2.195 r_angle_refined_deg 1.516 r_mcbond_it 1.457 r_mcbond_other 1.457 r_angle_other_deg 0.933 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 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 3427 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing