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Atomic resolution crystal structure of a cytochrome c-calixarene complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TYI pdb entry 3TYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293.15 18 % PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.49 50.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.11 α = 90 b = 55.78 β = 90 c = 119.08 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 100 CCD MARMOSAIC 225 mm CCD Pt coated mirrors 2011-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.05 15.39 94.9 0.113 9.1 6 113051 107285 2.5 6.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.11 100 0.962 1.8 5.4 16317
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 3TYI 1.05 15.39 107285 101839 5357 94.82 0.15813 0.15701 0.1578 0.17976 0.181 RANDOM 11.299
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] -0.43 0.2 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.122 r_sphericity_free 22.839 r_dihedral_angle_4_deg 22.131 r_dihedral_angle_3_deg 11.329 r_sphericity_bonded 6.913 r_dihedral_angle_1_deg 5.868 r_angle_refined_deg 1.266 r_rigid_bond_restr 1.264 r_chiral_restr 0.284 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.122 r_sphericity_free 22.839 r_dihedral_angle_4_deg 22.131 r_dihedral_angle_3_deg 11.329 r_sphericity_bonded 6.913 r_dihedral_angle_1_deg 5.868 r_angle_refined_deg 1.266 r_rigid_bond_restr 1.264 r_chiral_restr 0.284 r_gen_planes_refined 0.009 r_bond_refined_d 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1692 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 230
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling