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Crystal structure of uPA in complex with 3,5-bis(azanyl)-N-carbamimidoyl-6-(2,4-dimethoxypyrimidin-5-yl)pyrazine-2-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 50mM sodium citrate, pH 4.6, 2.0M ammonium sulfate supplemented with 5% polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 2.15 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.892 α = 90 b = 120.892 β = 90 c = 42.268 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 PIXEL DECTRIS PILATUS3 S 6M 2018-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.979 NFPSS BL19U1
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 2.48 60.45 99.1 0.142 17.3 4.8 8040
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 2.5 2.54 0.558
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 4DVA 2.48 60.45 7620 420 98.8 0.2 0.196 0.2 0.267 0.2684 RANDOM 47.81
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] -1.45 -0.72 -1.45 4.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.246 r_dihedral_angle_3_deg 16.975 r_dihedral_angle_4_deg 14.947 r_dihedral_angle_1_deg 8.383 r_long_range_B_refined 7.864 r_scangle_other 5.292 r_mcangle_it 4.775 r_mcangle_other 4.773 r_scbond_it 3.293 r_scbond_other 3.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.246 r_dihedral_angle_3_deg 16.975 r_dihedral_angle_4_deg 14.947 r_dihedral_angle_1_deg 8.383 r_long_range_B_refined 7.864 r_scangle_other 5.292 r_mcangle_it 4.775 r_mcangle_other 4.773 r_scbond_it 3.293 r_scbond_other 3.291 r_mcbond_other 2.995 r_mcbond_it 2.994 r_angle_refined_deg 1.632 r_angle_other_deg 0.965 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1933 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing