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The crystal structure of upain-1-W3A in complex with 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 50 mM sodium citrate pH 4.6, 2.0 M ammonium sulfate supplemented with 5% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.149 α = 90 b = 121.149 β = 90 c = 42.914 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 MARMOSAIC 325 mm CCD 2009-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.29 50 97.5 33.2 5 57598
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 1.29 50 54671 2910 97.58 0.211 0.21026 0.2101 0.22497 0.227 RANDOM 16.784
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] -0.17 -0.08 -0.17 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.365 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_4_deg 10.425 r_dihedral_angle_1_deg 6.073 r_scangle_it 2.915 r_scbond_it 1.836 r_mcangle_it 1.313 r_angle_refined_deg 1.236 r_mcbond_it 0.702 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.365 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_4_deg 10.425 r_dihedral_angle_1_deg 6.073 r_scangle_it 2.915 r_scbond_it 1.836 r_mcangle_it 1.313 r_angle_refined_deg 1.236 r_mcbond_it 0.702 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other 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 1979 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling Coot model building