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Shewanella denitrificans nitrous oxide reductase, reduced apo 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 8.5 298 25% PEG 3350
0.2 M lithium sulphate
0.1 M Tris/HCl
Crystal Properties Matthews coefficient Solvent content 2.11 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.101 α = 90 b = 121.459 β = 90 c = 172.4 γ = 90
Symmetry Space Group P 2 21 21
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 PILATUS3 6M 2015-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
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 2.55 172.4 100 0.996 10.8 12.5 40073
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 2.55 99.29 38052 1964 99.99 0.18962 0.18772 0.2278 0.2192 RANDOM 38.803
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] -3.38 0.33 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.623 r_dihedral_angle_4_deg 19.025 r_dihedral_angle_3_deg 14.304 r_dihedral_angle_1_deg 6.937 r_long_range_B_refined 5.018 r_long_range_B_other 5.012 r_scangle_other 3.048 r_mcangle_it 2.599 r_mcangle_other 2.599 r_scbond_it 1.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.623 r_dihedral_angle_4_deg 19.025 r_dihedral_angle_3_deg 14.304 r_dihedral_angle_1_deg 6.937 r_long_range_B_refined 5.018 r_long_range_B_other 5.012 r_scangle_other 3.048 r_mcangle_it 2.599 r_mcangle_other 2.599 r_scbond_it 1.764 r_scbond_other 1.764 r_mcbond_it 1.503 r_mcbond_other 1.503 r_angle_refined_deg 1.427 r_angle_other_deg 1.03 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 8343 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing