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The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH7.4
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% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.17 43.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.575 α = 90 b = 121.575 β = 90 c = 42.212 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 2012-06-13 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 2 99 99.5 0.061 32.6 3.7 15624
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 0.503
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 60.79 14847 777 99.24 0.21431 0.21192 0.2128 0.26158 0.2511 RANDOM 55.99
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] 0.27 0.13 0.27 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.327 r_dihedral_angle_3_deg 15.857 r_dihedral_angle_4_deg 14.568 r_long_range_B_refined 9.281 r_long_range_B_other 9.25 r_dihedral_angle_1_deg 6.615 r_scangle_other 5.459 r_mcangle_it 4.481 r_mcangle_other 4.48 r_scbond_it 3.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.327 r_dihedral_angle_3_deg 15.857 r_dihedral_angle_4_deg 14.568 r_long_range_B_refined 9.281 r_long_range_B_other 9.25 r_dihedral_angle_1_deg 6.615 r_scangle_other 5.459 r_mcangle_it 4.481 r_mcangle_other 4.48 r_scbond_it 3.513 r_scbond_other 3.498 r_mcbond_it 2.905 r_mcbond_other 2.895 r_angle_refined_deg 1.297 r_angle_other_deg 0.889 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 1942 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing