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Crystal structure of cytochrome c in complex with mono-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, and 0.1 M Sodium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.88 57.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.3 α = 90 b = 149.3 β = 90 c = 149.3 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 EIGER X 9M 2016-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
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 2.7 105.57 100 0.09 0.98 6.9 37.4 8115
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 2.7 2.83 100 0.605 0.498 1.4 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 2.7 105.57 7707 386 99.94 0.2285 0.2262 0.2285 0.2731 0.2795 RANDOM 52.502
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 35.064 r_dihedral_angle_4_deg 25.654 r_dihedral_angle_3_deg 13.813 r_dihedral_angle_1_deg 6.073 r_angle_refined_deg 1.296 r_angle_other_deg 0.878 r_chiral_restr 0.084 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.064 r_dihedral_angle_4_deg 25.654 r_dihedral_angle_3_deg 13.813 r_dihedral_angle_1_deg 6.073 r_angle_refined_deg 1.296 r_angle_other_deg 0.878 r_chiral_restr 0.084 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1692 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 363
Software Software Software Name Purpose REFMAC refinement MOSFLM data collection Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction