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4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 crystallisation solution: 50 mM NaAcetate, 0.25 M NaCl, 4 mM MMTS, 30% PEG 4K, 0.1 M NaCitrate, 0,2 M (NH4)2SO4, 10 mM DMSO, 10 mM DTT. Cryoprotectant composition: 30% PEG 4K, 0.1 M NaCitrate, 0.2 M (NH4)2SO4, 15% PEG 400 (+ 10% compound). Ligand was introduced by soaking crystals prepared with another compound, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.89 57.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.757 α = 90 b = 85.757 β = 90 c = 150.902 γ = 90
Symmetry Space Group P 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE RIGAKU RAXIS IV 2007-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 85.75 87.7 0.166 5.3 5.28 65361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 24.9 0.501 1.1 1.41 1825
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 74.56 65283 3289 87.78 0.225 0.223 0.2262 0.264 0.2663 RANDOM 24.555
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] -0.03 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.388 r_dihedral_angle_4_deg 24.167 r_dihedral_angle_3_deg 11.873 r_dihedral_angle_1_deg 5.591 r_scangle_it 1.971 r_scbond_it 1.347 r_angle_refined_deg 1.145 r_angle_other_deg 0.871 r_mcangle_it 0.839 r_mcbond_it 0.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.388 r_dihedral_angle_4_deg 24.167 r_dihedral_angle_3_deg 11.873 r_dihedral_angle_1_deg 5.591 r_scangle_it 1.971 r_scbond_it 1.347 r_angle_refined_deg 1.145 r_angle_other_deg 0.871 r_mcangle_it 0.839 r_mcbond_it 0.553 r_symmetry_vdw_other 0.25 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.19 r_nbd_other 0.189 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.144 r_mcbond_other 0.104 r_nbtor_other 0.085 r_chiral_restr 0.062 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3372 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 100
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction