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Crystal Structure of Cytochrome c in complex with p-Methylphosphonatocalix[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 5.6 293 20 % PEG 8000, 50 mM NaCl, 50 mM sodium acetate (pH 5.6). [Cytochrome c] = 0.75 mM and [Methylphosphonatocalix[4]arene] = 0.3 mM
Crystal Properties Matthews coefficient Solvent content 2.39 48.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.917 α = 90 b = 80.227 β = 93.07 c = 47.807 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M-F 2016-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 47.74 99.2 0.055 0.026 0.999 18.7 5.5 34591
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 1.5 1.55 99.4 0.055 0.158 5.1 5.4
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 1.5 47.74 32897 1707 99.23 0.1719 0.1704 0.1746 0.2012 0.2047 RANDOM 20.624
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] 0.3 -2.11 -0.88 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.978 r_dihedral_angle_4_deg 24.671 r_dihedral_angle_3_deg 14.117 r_dihedral_angle_1_deg 6.26 r_angle_refined_deg 1.608 r_angle_other_deg 1.012 r_chiral_restr 0.122 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.978 r_dihedral_angle_4_deg 24.671 r_dihedral_angle_3_deg 14.117 r_dihedral_angle_1_deg 6.26 r_angle_refined_deg 1.608 r_angle_other_deg 1.012 r_chiral_restr 0.122 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.011 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1624 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 295
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing