☰ Navigation Tabs
Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK903
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.25 291 20% PEG4000, 16% glycerol, 0.17 M ammonium sulfate, 0.1 M sodium acetate, pH 4.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.959 α = 90 b = 54.457 β = 98.18 c = 71.681 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 PIXEL DECTRIS PILATUS 2M-F 2013-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 1.7 45.68 100 0.065 10.5 3.3 56805 56805 15.3
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 1.7 1.79 92.5 0.386 2.5 2.8 7709
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 43.24 56805 53950 2847 98.5 0.16799 0.16799 0.16557 0.21471 0.2175 RANDOM 20.091
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] 2 -0.88 -1.14 -0.71
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.391 r_dihedral_angle_2_deg 32.235 r_dihedral_angle_4_deg 19.446 r_dihedral_angle_3_deg 13.944 r_sphericity_bonded 11.133 r_dihedral_angle_1_deg 6.23 r_rigid_bond_restr 4.422 r_angle_refined_deg 1.277 r_angle_other_deg 0.923 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.391 r_dihedral_angle_2_deg 32.235 r_dihedral_angle_4_deg 19.446 r_dihedral_angle_3_deg 13.944 r_sphericity_bonded 11.133 r_dihedral_angle_1_deg 6.23 r_rigid_bond_restr 4.422 r_angle_refined_deg 1.277 r_angle_other_deg 0.923 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4058 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 94
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling