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X-ray crystallographic study of PIYDIN, which contains the truncation determinants of binding PI and N, bound to RoAb13, a CCR5 antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S2S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 10 mg/ml protein, 20 mM HEPES pH 7.0, 0.1 M sodium chloride, 660 uM PIYDIN peptide, 1.8 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.02 69.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.607 α = 90 b = 76.607 β = 90 c = 270.06 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS 6M-F 2018-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 3.2 270.06 99.9 0.179 0.183 0.037 0.999 14.3 24.8 14151 135.11414236
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 1.228 0.529 0.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4S2S 3.20001097294 67.515 1.34416359481 14069 728 99.8864039759 0.269545672354 0.268273678187 0.2766 0.292693257892 0.3109 173.688789619
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.1544808982 f_angle_d 0.7915570813 f_chiral_restr 0.0478509479134 f_plane_restr 0.0047339297548 f_bond_d 0.00401374492547
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3324 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing