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Crystal structure of cytochrome c in complex with di-PEGylated sulfonatocalix[4]arene
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 1.6 M Sodium Citrate, 0.1 M Sodium Chloride, 0.1 M Sodium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.961 α = 90 b = 147.961 β = 90 c = 147.961 γ = 90
Symmetry Space Group I 41 3 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 PILATUS3 S 6M 2016-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97911 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.17 104.62 99.9 0.025 1 22.5 37.4 14898
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.24 98.9 1.29 0.595 0.7 33.8
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 2.17 104.62 13879 729 98.14 0.2046 0.2025 0.2079 0.2475 0.2519 RANDOM 63.515
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.106 r_dihedral_angle_4_deg 30.165 r_dihedral_angle_3_deg 15.483 r_dihedral_angle_1_deg 6.099 r_angle_refined_deg 1.461 r_angle_other_deg 0.952 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.106 r_dihedral_angle_4_deg 30.165 r_dihedral_angle_3_deg 15.483 r_dihedral_angle_1_deg 6.099 r_angle_refined_deg 1.461 r_angle_other_deg 0.952 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1692 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 223
Software Software Software Name Purpose XDS data collection XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction