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Structure of PAItrap, an uPA mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 2.2 M ammonium sulfate, 5% PEG 400, 50 mM sodium citrate (pH 4.6)
Crystal Properties Matthews coefficient Solvent content 2.17 43.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.025 α = 90 b = 121.025 β = 90 c = 42.774 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 280 CCD ADSC QUANTUM 315r 2013-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
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 1.5 34.94 99.82 27 2
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 4H42 1.5 34.94 35505 1869 99.81 0.1757 0.17394 0.174 0.20865 0.2088 RANDOM 18.238
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] -0.09 -0.05 -0.09 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.697 r_dihedral_angle_4_deg 22.298 r_dihedral_angle_3_deg 14.518 r_dihedral_angle_1_deg 7.657 r_long_range_B_refined 5.984 r_long_range_B_other 5.983 r_scangle_other 4.459 r_scbond_it 3.093 r_scbond_other 3.092 r_mcangle_it 2.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.697 r_dihedral_angle_4_deg 22.298 r_dihedral_angle_3_deg 14.518 r_dihedral_angle_1_deg 7.657 r_long_range_B_refined 5.984 r_long_range_B_other 5.983 r_scangle_other 4.459 r_scbond_it 3.093 r_scbond_other 3.092 r_mcangle_it 2.551 r_mcangle_other 2.55 r_angle_refined_deg 2.219 r_mcbond_it 1.8 r_mcbond_other 1.797 r_angle_other_deg 0.98 r_chiral_restr 0.131 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 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 1945 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP model building