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Shewanella denitrificans nitrous oxide reductase, Ca2+-reconstituted form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 25 % PEG 3350
0.2 M ammonium sulfate
0.1 M Bis-tris/HCl
Crystal Properties Matthews coefficient Solvent content 1.97 37.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.756 α = 90 b = 56.978 β = 105.58 c = 163.524 γ = 90
Symmetry Space Group C 1 2 1
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 2M 2015-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.37 47.35 99.3 0.999 13.4 6.2 219234
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 5i5i 1.37 157.52 219234 11354 99.33 0.16417 0.16331 0.18067 0.1753 RANDOM 9.597
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] 0.39 -0.33 -0.38 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.763 r_dihedral_angle_4_deg 13.794 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_1_deg 6.758 r_long_range_B_refined 3.367 r_long_range_B_other 3.117 r_angle_refined_deg 1.617 r_scangle_other 1.288 r_angle_other_deg 1.006 r_mcangle_it 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.763 r_dihedral_angle_4_deg 13.794 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_1_deg 6.758 r_long_range_B_refined 3.367 r_long_range_B_other 3.117 r_angle_refined_deg 1.617 r_scangle_other 1.288 r_angle_other_deg 1.006 r_mcangle_it 0.886 r_mcangle_other 0.886 r_scbond_it 0.811 r_scbond_other 0.805 r_mcbond_it 0.516 r_mcbond_other 0.515 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 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 9033 Nucleic Acid Atoms Solvent Atoms 1053 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing