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The crystal structure of uPA in complex with 4-Iodobenzylamine at pH7.4
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 50mM sodium citrate (pH 4.6), 2.0M ammonium sulfate supplemented with 5% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.16 43.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.503 α = 90 b = 120.503 β = 90 c = 42.719 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 2014-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
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 1.45 50 97.9 0.048 22.7 3.7 40221
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 1.45 1.5 0.882
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 1.45 34.79 38246 1967 97.79 0.11911 0.11791 0.1231 0.14284 0.1501 RANDOM 30.576
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] -0.2 -0.1 -0.2 0.65
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.523 r_dihedral_angle_2_deg 34.285 r_sphericity_bonded 21.265 r_dihedral_angle_3_deg 14.029 r_dihedral_angle_4_deg 13.405 r_long_range_B_refined 8.089 r_long_range_B_other 7.963 r_scangle_other 7.812 r_scbond_it 7.069 r_scbond_other 6.923
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.523 r_dihedral_angle_2_deg 34.285 r_sphericity_bonded 21.265 r_dihedral_angle_3_deg 14.029 r_dihedral_angle_4_deg 13.405 r_long_range_B_refined 8.089 r_long_range_B_other 7.963 r_scangle_other 7.812 r_scbond_it 7.069 r_scbond_other 6.923 r_dihedral_angle_1_deg 6.38 r_mcangle_other 6.226 r_mcangle_it 6.214 r_mcbond_it 5.244 r_mcbond_other 5.222 r_rigid_bond_restr 1.811 r_angle_refined_deg 1.402 r_angle_other_deg 0.979 r_chiral_restr 0.084 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.01 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1933 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing