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Crystal structure of uPA in complex with upain-2-4-W3A
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 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.874 α = 90 b = 120.874 β = 90 c = 42.958 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 2014-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF 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 1.75 50 99.9 0.073 25.8 10 23685
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 1.75 50 22209 1152 98.3 0.196 0.194 0.1999 0.234 0.2351 RANDOM 21.6
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] -0.05 -0.02 -0.05 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.553 r_dihedral_angle_4_deg 14.816 r_dihedral_angle_3_deg 12.968 r_dihedral_angle_1_deg 6.096 r_long_range_B_refined 4.097 r_long_range_B_other 3.939 r_mcangle_it 1.905 r_mcangle_other 1.904 r_scangle_other 1.668 r_angle_refined_deg 1.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.553 r_dihedral_angle_4_deg 14.816 r_dihedral_angle_3_deg 12.968 r_dihedral_angle_1_deg 6.096 r_long_range_B_refined 4.097 r_long_range_B_other 3.939 r_mcangle_it 1.905 r_mcangle_other 1.904 r_scangle_other 1.668 r_angle_refined_deg 1.184 r_mcbond_other 1.051 r_mcbond_it 1.05 r_scbond_it 0.958 r_scbond_other 0.958 r_angle_other_deg 0.868 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2025 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing