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The crystal structure of mupain-1-12 in complex with murinised human uPA 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 4.6 298 2.0M ammonium sulfate, 50mM sodium citrate pH 4.6, 5% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.06 40.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.177 α = 90 b = 121.177 β = 90 c = 42.368 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 210 2012-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.0 BSRF 3W1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 98.9 29.4 3.4 13394
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 2.1 35.01 12726 664 98.79 0.21327 0.21036 0.2116 0.27282 0.2829 RANDOM 57.458
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] -0.51 -0.51 -0.51 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.404 r_dihedral_angle_3_deg 16.47 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_1_deg 6.634 r_angle_refined_deg 1.285 r_angle_other_deg 0.752 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.404 r_dihedral_angle_3_deg 16.47 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_1_deg 6.634 r_angle_refined_deg 1.285 r_angle_other_deg 0.752 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 2028 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Coot model building