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Cytochrome c co-crystallized with 20 eq. sulfonato-calix[8]arene and soaked with 25 eq. spermine - structure I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GD9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.10 M HEPES pH 7.5, 0.15 M NaCl, 2.2 M Ammonium sulfate, 0.04 M sulfonato-calix[8]arene
Crystal Properties Matthews coefficient Solvent content 85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.452 α = 90 b = 101.452 β = 90 c = 85.612 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 2018-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98008 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.268 71.737 100 0.094 0.019 25.7 26.5 21272 62.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.268 2.307 1.801 0.346
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 FREE R-VALUE 6GD9 2.27 54.99 21271 1061 100 0.194 0.193 0.1807 0.212 0.1901 RANDOM 59.75
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] 3.6815 3.6815 -7.363
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.18 t_omega_torsion 3.51 t_angle_deg 1.16 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.18 t_omega_torsion 3.51 t_angle_deg 1.16 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 846 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 399
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing