☰ Navigation Tabs
Room temperature crystal structure of cytochrome c' from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M HEPES pH 7, 0.2 M sodium chloride, 20% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.19 43.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.535 α = 90 b = 38.986 β = 97.24 c = 41.525 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 293 PIXEL DECTRIS EIGER2 X 4M 2022-04-13 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 1.75 35.14 93.9 0.151 0.17 0.076 1 9.9 4.4 12429 15.38
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 1.75 1.78 74.7 1.171 1.398 0.74 0.4 0.9
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 7EAD 1.75 35.14 11811 614 93.9 0.16013 0.15839 0.1668 0.19334 0.1957 RANDOM 23.947
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] -0.76 -0.07 -0.52 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.304 r_dihedral_angle_4_deg 21.208 r_dihedral_angle_3_deg 15.183 r_dihedral_angle_1_deg 6.957 r_long_range_B_refined 5.419 r_long_range_B_other 5.364 r_scangle_other 4.387 r_mcangle_it 2.907 r_mcangle_other 2.906 r_scbond_other 2.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.304 r_dihedral_angle_4_deg 21.208 r_dihedral_angle_3_deg 15.183 r_dihedral_angle_1_deg 6.957 r_long_range_B_refined 5.419 r_long_range_B_other 5.364 r_scangle_other 4.387 r_mcangle_it 2.907 r_mcangle_other 2.906 r_scbond_other 2.722 r_scbond_it 2.718 r_angle_refined_deg 2.229 r_mcbond_it 1.88 r_mcbond_other 1.872 r_angle_other_deg 1.32 r_chiral_restr 0.144 r_gen_planes_other 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 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 1058 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2.multiplex data scaling PHASER phasing