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Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form soaked with Spermine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2.1 M ammonium sulfate
0.1 M MES pH 6.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.252 α = 90 b = 101.252 β = 90 c = 85.31 γ = 90
Symmetry Space Group P 43 21 2
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 9M 2017-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980 SOLEIL PROXIMA 2
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 2.8 85.31 100 0.123 0.131 0.045 0.997 12.1 8.2 11454
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 2.8 2.95 100 0.666 0.71 0.243 0.473 8.5
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 1YCC 2.8 71.7 10844 570 100 0.223 0.2219 0.2248 0.243 0.2382 RANDOM 68.516
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] -1.47 -1.47 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.912 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_4_deg 10.923 r_dihedral_angle_1_deg 5.189 r_angle_refined_deg 1.192 r_angle_other_deg 0.714 r_chiral_restr 0.065 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.912 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_4_deg 10.923 r_dihedral_angle_1_deg 5.189 r_angle_refined_deg 1.192 r_angle_other_deg 0.714 r_chiral_restr 0.065 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 846 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 404
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction