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Structure of cytochrome c in complex with a p-benzyl-sulfonato-calix[8]arene-PEG pseudorotaxane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RSL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20 % PEG 3350
200mM Ammonium formate
Crystal Properties Matthews coefficient Solvent content 3.01 59.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.851 α = 90 b = 70.215 β = 102.93 c = 70.175 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 100 PIXEL DECTRIS EIGER2 X 9M 2019-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98009 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 3.02 50.57 96.3 0.222 0.241 0.093 0.991 8.9 6.7 10928 90.54
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 3.02 3.19 99.8 1.153 1.262 0.504 0.855 6.1
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 6RSL 3.023 50.57 10831 502 95.4 0.2346 0.2334 0.2466 0.2606 0.2741 RANDOM 75.3
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] -34.7443 -9.2754 14.8287 19.9156
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.11 t_omega_torsion 2.44 t_angle_deg 0.65 t_bond_d 0.005 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.11 t_omega_torsion 2.44 t_angle_deg 0.65 t_bond_d 0.005 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 3364 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 715
Software Software Software Name Purpose Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing