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Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with ammonium sulfate
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, HANGING DROP 293 1.75 M ammonium sulfate
0.2 M NaCl
(2x protein solution : 1x crystallisation condition)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.003 α = 90 b = 82.003 β = 90 c = 82.535 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 1.2 35.68 99.8 0.055 0.064 0.032 0.998 9.9 3.7 64600
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 1.2 1.22 99.5 0.533 0.636 0.341 0.735 3.3
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 1.2 35.68 61332 3238 99.76 0.1197 0.1189 0.1253 0.1361 0.1395 RANDOM 18.231
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] 0.08 0.04 0.08 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.406 r_sphericity_free 24.714 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 11.771 r_sphericity_bonded 8.366 r_dihedral_angle_1_deg 6.461 r_angle_refined_deg 1.48 r_rigid_bond_restr 0.961 r_angle_other_deg 0.873 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.406 r_sphericity_free 24.714 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 11.771 r_sphericity_bonded 8.366 r_dihedral_angle_1_deg 6.461 r_angle_refined_deg 1.48 r_rigid_bond_restr 0.961 r_angle_other_deg 0.873 r_chiral_restr 0.096 r_gen_planes_refined 0.013 r_gen_planes_other 0.013 r_bond_refined_d 0.011 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 846 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction