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Plasminogen activator inhibitor type-1 in complex with the inhibitor AZ3976
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DVN PDB ENTRY 1DVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 PAI-1 WAS CONCENTRATED TO ABOUT 4 G/L IN A BUFFER CONTAINING 10 MM SODIUM ACETATE PH 5.6, 150 MM SODIUM CHLORIDE AND 1 MM EDTA. AZ3976 WAS DISSOLVED IN DEUTERATED DMSO AND ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.3 MM. CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION TECHNIQUE: 2.5 UL PROTEIN SAMPLE WAS MIXED WITH 1 UL OF A WELL SOLUTION CONTAINING 2.0 M SODIUM CHLORIDE, 100 MM BIS-TRIS PH 6.8
Crystal Properties Matthews coefficient Solvent content 3.2 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.399 α = 90 b = 119.399 β = 90 c = 99.691 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 225 mm CCD 2010-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.4 49.9 100 0.1 16 5.9 62179 2
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 2.4 2.46 100 0.7 2.4 5.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DVN 2.4 60.01 58169 3163 98.67 0.15867 0.15743 0.18138 0.1848 RANDOM 45.905
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] 4.45 4.45 -8.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.198 r_dihedral_angle_4_deg 19.41 r_dihedral_angle_3_deg 17.641 r_dihedral_angle_1_deg 5.464 r_scangle_it 3.793 r_scbond_it 2.358 r_mcangle_it 1.564 r_angle_refined_deg 1.485 r_mcbond_it 0.826 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.198 r_dihedral_angle_4_deg 19.41 r_dihedral_angle_3_deg 17.641 r_dihedral_angle_1_deg 5.464 r_scangle_it 3.793 r_scbond_it 2.358 r_mcangle_it 1.564 r_angle_refined_deg 1.485 r_mcbond_it 0.826 r_chiral_restr 0.099 r_bond_refined_d 0.014 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 9115 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing