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Dimeric Shewanella violacea cytochrome c5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20% PEG 3350 and 200 mM potassium nitrate
Crystal Properties Matthews coefficient Solvent content 2.28 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.772 α = 90 b = 52.542 β = 90 c = 80.07 γ = 90
Symmetry Space Group P 21 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 EIGER X 4M 2019-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.15 43.93 96.7 0.031 0.999 26.1 6.5 51052
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.17 83.5 0.323 0.882 4.2 4.6
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 5B6Q 1.15 31.91 48427 2575 96.31 0.13924 0.13829 0.1399 0.15703 0.1655 RANDOM 13.421
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] 2.33 1.75 -4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.621 r_dihedral_angle_4_deg 15.542 r_dihedral_angle_3_deg 11.409 r_dihedral_angle_1_deg 5.965 r_rigid_bond_restr 3.523 r_long_range_B_refined 2.705 r_angle_refined_deg 2.451 r_long_range_B_other 1.875 r_angle_other_deg 1.51 r_scangle_other 1.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.621 r_dihedral_angle_4_deg 15.542 r_dihedral_angle_3_deg 11.409 r_dihedral_angle_1_deg 5.965 r_rigid_bond_restr 3.523 r_long_range_B_refined 2.705 r_angle_refined_deg 2.451 r_long_range_B_other 1.875 r_angle_other_deg 1.51 r_scangle_other 1.202 r_mcangle_it 1.025 r_mcangle_other 1.024 r_scbond_it 0.963 r_scbond_other 0.957 r_mcbond_it 0.708 r_mcbond_other 0.707 r_chiral_restr 0.161 r_gen_planes_other 0.016 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1110 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing