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Potent and selective bicyclic peptide inhibitor (UK18) of human urokinase-type plasminogen activator(uPA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NWN 2NWN.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.3 293 2M ammonium sulfate, 0.05M sodium citrate, 5%(v/v) PEG 400, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.25 α = 90 b = 121.25 β = 90 c = 42.72 γ = 120
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 ADSC QUANTUM 315r Toroidal focusing mirrors 2010-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
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 1.9 39.57 99.8 0.079 12.2 5.4 18155 18155
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 1.9 2 100 0.405 3.9 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2NWN.pdb 1.9 39.57 18155 17487 946 99.76 0.19822 0.19822 0.19527 0.1959 0.25233 0.2505 RANDOM 34.287
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] -0.96 -0.48 -0.96 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.911 r_dihedral_angle_4_deg 19.594 r_dihedral_angle_3_deg 16.772 r_dihedral_angle_1_deg 7.462 r_scangle_it 4.94 r_scbond_it 3.22 r_mcangle_it 2.344 r_angle_refined_deg 1.9 r_mcbond_it 1.329 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.911 r_dihedral_angle_4_deg 19.594 r_dihedral_angle_3_deg 16.772 r_dihedral_angle_1_deg 7.462 r_scangle_it 4.94 r_scbond_it 3.22 r_mcangle_it 2.344 r_angle_refined_deg 1.9 r_mcbond_it 1.329 r_chiral_restr 0.154 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2050 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 9
Software Software Software Name Purpose ADSC data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling