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Crystal structure of uPA in complex with upain-2-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NWN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 50 mM sodium citrate, pH 4.6, and 2.0 M ammonium sulfate supplemented with 5% polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 1.81 31.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.137 α = 90 b = 115.137 β = 90 c = 41.307 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 1.46 57.57 99.5 0.062 36.4 4.1 35325
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 2NWN 1.46 57.57 33554 1770 99.9 0.211 0.209 0.2014 0.245 0.2375 RANDOM 18.78
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] -0.19 -0.1 -0.19 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.899 r_dihedral_angle_3_deg 14.978 r_dihedral_angle_4_deg 14.21 r_dihedral_angle_1_deg 6.858 r_scangle_it 3.312 r_scbond_it 2.094 r_angle_refined_deg 1.598 r_mcangle_it 1.537 r_rigid_bond_restr 0.997 r_mcbond_it 0.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.899 r_dihedral_angle_3_deg 14.978 r_dihedral_angle_4_deg 14.21 r_dihedral_angle_1_deg 6.858 r_scangle_it 3.312 r_scbond_it 2.094 r_angle_refined_deg 1.598 r_mcangle_it 1.537 r_rigid_bond_restr 0.997 r_mcbond_it 0.844 r_chiral_restr 0.077 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2036 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing