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Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with PEG
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 5 % PEG 3350
(2x protein solution : 1x crystallisation condition)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.42 α = 90 b = 81.42 β = 90 c = 82.364 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) 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 1.55 40.71 99.9 0.056 0.026 1 12.8 4.4 29520
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 99.9 0.516 0.256 0.49 3.9
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 1.55 40.71 28013 1501 99.88 0.151 0.1493 0.1593 0.1835 0.1941 RANDOM 30.532
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] 0.56 0.28 0.56 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.404 r_dihedral_angle_4_deg 24.262 r_dihedral_angle_3_deg 12.815 r_sphericity_bonded 7.767 r_dihedral_angle_1_deg 5.673 r_rigid_bond_restr 1.604 r_angle_refined_deg 1.437 r_angle_other_deg 0.973 r_chiral_restr 0.088 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.404 r_dihedral_angle_4_deg 24.262 r_dihedral_angle_3_deg 12.815 r_sphericity_bonded 7.767 r_dihedral_angle_1_deg 5.673 r_rigid_bond_restr 1.604 r_angle_refined_deg 1.437 r_angle_other_deg 0.973 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 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 846 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 145
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction