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Crystal structure of uPA in complex with upain-2-2-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 2.07 40.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.07 α = 90 b = 121.07 β = 90 c = 42.88 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 2010-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
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 1.64 24.07 98.3 0.043 17.2 3.5 28216
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 1.64 24.07 26795 1420 98.3 0.182 0.18 0.1883 0.221 0.2274 RANDOM 27.45
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] -0.31 -0.31 -0.31 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.482 r_dihedral_angle_4_deg 16.535 r_dihedral_angle_3_deg 16.401 r_dihedral_angle_1_deg 7.218 r_angle_refined_deg 2.026 r_angle_other_deg 0.952 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.482 r_dihedral_angle_4_deg 16.535 r_dihedral_angle_3_deg 16.401 r_dihedral_angle_1_deg 7.218 r_angle_refined_deg 2.026 r_angle_other_deg 0.952 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2027 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing