☰ Navigation Tabs
The crystal structure of uPA in complex with HMA-55F
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 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.94 α = 90 b = 120.94 β = 90 c = 42.795 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 PILATUS 6M 2015-03-29 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 1.9 60 100 0.109 21.6 4.9 18351
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 1.9 1.93 0.557
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 1.9 60 17446 905 99.79 0.19926 0.19769 0.2005 0.22847 0.2241 RANDOM 35.086
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] -0.61 -0.31 -0.61 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.12 r_dihedral_angle_4_deg 21.647 r_dihedral_angle_3_deg 14.714 r_dihedral_angle_1_deg 6.771 r_long_range_B_refined 5.281 r_long_range_B_other 5.264 r_scangle_other 3.067 r_mcangle_it 2.694 r_mcangle_other 2.694 r_scbond_it 1.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.12 r_dihedral_angle_4_deg 21.647 r_dihedral_angle_3_deg 14.714 r_dihedral_angle_1_deg 6.771 r_long_range_B_refined 5.281 r_long_range_B_other 5.264 r_scangle_other 3.067 r_mcangle_it 2.694 r_mcangle_other 2.694 r_scbond_it 1.807 r_scbond_other 1.807 r_mcbond_it 1.605 r_mcbond_other 1.6 r_angle_refined_deg 1.345 r_angle_other_deg 0.89 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1933 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing