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Native cytochrome c6 from Thermosynechococcus elongatus in space group H3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 278 Ammonium sulfate, potassium nitrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.8 α = 90 b = 94.8 β = 90 c = 160.22 γ = 120
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 PILATUS 6M 2019-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.189 73.065 98.5 0.101 0.12 0.064 4.7 3.1 170023 170023
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.25 98.7 1.555 1.555 1.873 1.026 0.5 3.1
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 4EIC 1.7 36.53 55146 2864 98.22 0.1868 0.1857 0.1994 0.2078 0.2167 RANDOM 21.067
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] 3.3 3.3 -6.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.698 r_dihedral_angle_4_deg 35.86 r_dihedral_angle_3_deg 16.503 r_dihedral_angle_1_deg 6.36 r_angle_refined_deg 2.804 r_angle_other_deg 1.281 r_chiral_restr 0.207 r_bond_refined_d 0.032 r_gen_planes_refined 0.02 r_gen_planes_other 0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.698 r_dihedral_angle_4_deg 35.86 r_dihedral_angle_3_deg 16.503 r_dihedral_angle_1_deg 6.36 r_angle_refined_deg 2.804 r_angle_other_deg 1.281 r_chiral_restr 0.207 r_bond_refined_d 0.032 r_gen_planes_refined 0.02 r_gen_planes_other 0.018 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1922 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing