☰ Navigation Tabs
Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ATK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Potassium chloride 0.2M,
HEPES 0.05M,
5/4 PO/OH 35%
Crystal Properties Matthews coefficient Solvent content 2.05 39.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.219 α = 90 b = 44.403 β = 116.42 c = 51.354 γ = 90
Symmetry Space Group P 1 21 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 CCD Bruker Platinum 135 2014-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.585 45.99 97.53 0.08534 0.991 9.12 1.9 25360
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.585 1.642 90.01 1.124 0.189 1.17 1.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ATK 1.59 45.99 49603 1246 97.43 0.1859 0.1832 0.1936 0.2376 0.2439 RANDOM 18.432
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] 0.41 0.51 -0.6 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.795 r_dihedral_angle_3_deg 14.68 r_dihedral_angle_4_deg 12.253 r_dihedral_angle_1_deg 6.428 r_mcangle_it 2.113 r_angle_refined_deg 1.925 r_mcbond_it 1.493 r_mcbond_other 1.49 r_angle_other_deg 1.458 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.795 r_dihedral_angle_3_deg 14.68 r_dihedral_angle_4_deg 12.253 r_dihedral_angle_1_deg 6.428 r_mcangle_it 2.113 r_angle_refined_deg 1.925 r_mcbond_it 1.493 r_mcbond_other 1.49 r_angle_other_deg 1.458 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1649 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction PROTEUM PLUS data reduction