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Crystal Structure of Cytochrome c - p-Sulfonatocalix[4]arene Complexes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YCC PDB ENTRY 1YCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293.15 26 % PEG 8000, 100 mM Magnesium Chloride, 50 mM Sodium Chloride, 50 mM Sodium Cacodylate pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.42 49.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.044 α = 90 b = 55.317 β = 90 c = 117.419 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 198.5 CCD MARMOSAIC 225 mm CCD 2011-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.13 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.399 50 98.7 0.044 0.044 36.811 4.3 47273 47273 -3 14.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.399 1.42 90.6 0.299 0.299 2.373 2.3 2082
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 1YCC 1.399 30.19 45566 954 98.43 0.17742 0.17696 0.1751 0.19848 0.1952 RANDOM 17.163
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] -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.133 r_dihedral_angle_4_deg 17.532 r_dihedral_angle_3_deg 13.652 r_dihedral_angle_1_deg 5.779 r_scangle_it 2.967 r_scbond_it 1.977 r_mcangle_it 1.309 r_angle_refined_deg 1.238 r_mcbond_it 0.686 r_chiral_restr 0.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.133 r_dihedral_angle_4_deg 17.532 r_dihedral_angle_3_deg 13.652 r_dihedral_angle_1_deg 5.779 r_scangle_it 2.967 r_scbond_it 1.977 r_mcangle_it 1.309 r_angle_refined_deg 1.238 r_mcbond_it 0.686 r_chiral_restr 0.287 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1688 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 230
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling