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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 3.8 67.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.657 α = 90 b = 77.657 β = 90 c = 87.855 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 2014-03-14 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 1.86 87.86 100 0.104 0.11 0.035 0.999 21.9 9.8 26331
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 1.86 2.08 100 0.389 0.411 0.131 0.966 9.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2xya 1.86 20 24961 1309 99.84 0.1496 0.1484 0.1719 0.1747 RANDOM 20.381
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] 0.37 0.19 0.37 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.309 r_dihedral_angle_4_deg 22.475 r_dihedral_angle_3_deg 11.471 r_dihedral_angle_1_deg 6.908 r_angle_refined_deg 1.693 r_angle_other_deg 1.031 r_chiral_restr 0.115 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.309 r_dihedral_angle_4_deg 22.475 r_dihedral_angle_3_deg 11.471 r_dihedral_angle_1_deg 6.908 r_angle_refined_deg 1.693 r_angle_other_deg 1.031 r_chiral_restr 0.115 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.014 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1415 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 81
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing