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The structure of the cytochrome c546/556 from Thioalkalivibrio paradoxus with unusual UV-Vis spectral features at atomic resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 288 0.1 M Citric acid, pH 3.5, 30% PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.416 α = 90 b = 37.601 β = 90 c = 97.117 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 PILATUS3 6M 2021-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.800 SPring-8 BL41XU
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 1.15 48.56 98.5 0.037 0.043 0.022 0.999 13.1 3.5 47379
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 1.15 1.17 95.7 0.174 0.206 0.108 0.922 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.15 48.56 45054 2275 97.99 0.11552 0.11406 0.1146 0.14417 0.1447 RANDOM 14.26
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] 0.11 0.01 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.361 r_dihedral_angle_3_deg 12.148 r_dihedral_angle_1_deg 5.933 r_rigid_bond_restr 3.772 r_long_range_B_refined 2.804 r_scangle_other 2.667 r_angle_refined_deg 2.629 r_long_range_B_other 2.543 r_scbond_other 2.287 r_scbond_it 2.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.361 r_dihedral_angle_3_deg 12.148 r_dihedral_angle_1_deg 5.933 r_rigid_bond_restr 3.772 r_long_range_B_refined 2.804 r_scangle_other 2.667 r_angle_refined_deg 2.629 r_long_range_B_other 2.543 r_scbond_other 2.287 r_scbond_it 2.285 r_mcangle_other 1.938 r_mcangle_it 1.879 r_dihedral_angle_4_deg 1.554 r_mcbond_it 1.425 r_mcbond_other 1.374 r_angle_other_deg 0.902 r_chiral_restr 0.179 r_bond_refined_d 0.02 r_gen_planes_other 0.02 r_gen_planes_refined 0.019 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1240 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CRANK2 phasing DIALS data reduction