☰ Navigation Tabs
Room temperature crystal structure of cytochrome c' from Hydrogenophilus thermoluteolus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B3I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 30% PEG 8000, 0.2 M lithium sulfate, 0.1 M sodium acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.536 α = 90 b = 83.536 β = 90 c = 88.566 γ = 120
Symmetry Space Group P 62 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER2 X 4M 2022-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.7749 Diamond VMXi
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.88 56.09 100 0.459 0.469 0.093 0.995 7.9 22.3 15440
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.91 100 5.496 5.683 1.401 0.258 0.6 15.4
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 5B3I 1.88 56.09 14620 777 99.9 0.17918 0.17791 0.1876 0.20314 0.2108 RANDOM 31.553
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] 0.04 0.02 0.04 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.968 r_dihedral_angle_4_deg 21.823 r_dihedral_angle_3_deg 17.295 r_long_range_B_refined 9.379 r_long_range_B_other 9.35 r_scangle_other 7.873 r_dihedral_angle_1_deg 5.893 r_scbond_it 5.247 r_scbond_other 5.095 r_mcangle_it 4.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.968 r_dihedral_angle_4_deg 21.823 r_dihedral_angle_3_deg 17.295 r_long_range_B_refined 9.379 r_long_range_B_other 9.35 r_scangle_other 7.873 r_dihedral_angle_1_deg 5.893 r_scbond_it 5.247 r_scbond_other 5.095 r_mcangle_it 4.162 r_mcangle_other 4.159 r_mcbond_it 2.763 r_mcbond_other 2.762 r_angle_refined_deg 2.32 r_angle_other_deg 1.481 r_chiral_restr 0.158 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1029 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2.multiplex data scaling PHASER phasing