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Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 2.0 M Ammonium Sulfate
0.1 M Na Acetate, pH 4.5,
Crystal Properties Matthews coefficient Solvent content 3.78 67.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.459 α = 90 b = 77.459 β = 90 c = 87.863 γ = 120
Symmetry Space Group P 32 2 1
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 2M 2014-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99988 SLS X10SA
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 1.75 67.08 100 0.126 0.133 0.043 0.999 15.4 9.7 31250
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 1.75 2.02 100 0.669 0.707 0.228 0.922 9.7
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 2xya 1.75 20 29638 1548 99.9 0.1501 0.149 0.1527 0.1695 0.1734 RANDOM 23.26
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] 0.21 0.1 0.21 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.386 r_dihedral_angle_4_deg 19.788 r_dihedral_angle_3_deg 11.99 r_dihedral_angle_1_deg 6.499 r_angle_refined_deg 1.602 r_angle_other_deg 0.808 r_chiral_restr 0.107 r_gen_planes_refined 0.021 r_gen_planes_other 0.017 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.386 r_dihedral_angle_4_deg 19.788 r_dihedral_angle_3_deg 11.99 r_dihedral_angle_1_deg 6.499 r_angle_refined_deg 1.602 r_angle_other_deg 0.808 r_chiral_restr 0.107 r_gen_planes_refined 0.021 r_gen_planes_other 0.017 r_bond_refined_d 0.01 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1415 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 56
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing