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Crystal structure of uPA-S195A in complex with S2444
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 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 2.17 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.354 α = 90 b = 121.354 β = 90 c = 42.207 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 2014-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.979 NFPSS 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 2.1 60 99.5 0.094 23.6 3.4 13398
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 2.1 30.36 12735 663 99.47 0.2159 0.21346 0.2138 0.266 0.2673 RANDOM 43.693
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] -0.12 -0.12 -0.12 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.049 r_dihedral_angle_4_deg 21.111 r_dihedral_angle_3_deg 17.503 r_dihedral_angle_1_deg 6.463 r_angle_refined_deg 1.361 r_angle_other_deg 0.734 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.049 r_dihedral_angle_4_deg 21.111 r_dihedral_angle_3_deg 17.503 r_dihedral_angle_1_deg 6.463 r_angle_refined_deg 1.361 r_angle_other_deg 0.734 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 1932 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing