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Cytochrome c in complex with Sulfonato-calix[8]arene, P31 form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LYC 5LYC chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 24 % PEG 3350
0.27 M NaCl
0.09 M MES pH 5.5
(2x protein solution : 1x crystallisation condition)
Crystal Properties Matthews coefficient Solvent content 3.81 67.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.68 α = 90 b = 66.68 β = 90 c = 142.881 γ = 120
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 2017-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.5 71.44 99.7 0.131 0.158 0.086 0.984 5.7 3.1 24569
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.9 0.39 0.47 0.259 0.607 3.1
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 5LYC chain A 2.5 57.75 23441 1090 99.75 0.1772 0.1761 0.1772 0.1998 0.192 RANDOM 41.858
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] 13.98 13.98 -27.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.034 r_dihedral_angle_4_deg 21.613 r_dihedral_angle_3_deg 12.728 r_dihedral_angle_1_deg 6.04 r_angle_refined_deg 1.375 r_angle_other_deg 0.903 r_chiral_restr 0.09 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.034 r_dihedral_angle_4_deg 21.613 r_dihedral_angle_3_deg 12.728 r_dihedral_angle_1_deg 6.04 r_angle_refined_deg 1.375 r_angle_other_deg 0.903 r_chiral_restr 0.09 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3384 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 497
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction