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Identification of small molecule inhibitors selective for apo(a) kringles KIV-7, KIV-10 and KV.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KIV PDB ENTRY 3KIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 30% PEG400, 0.1M CACL2, 0.1M NAOAC PH 4.6
Crystal Properties Matthews coefficient Solvent content 1.7 29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.41 α = 90 b = 45.25 β = 90.67 c = 56.1 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU A200-CU MIRRORS 2010-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+
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 2.1 28 95.4 0.03 5.9 6.4 6931 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 2.1 2.15 92 0.98 1.8 6.5
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 PDB ENTRY 3KIV 2.1 28.06 6303 314 91.23 0.19187 0.18986 0.1907 0.23013 0.2328 RANDOM 12.524
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] -0.29 -0.31 -0.88 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.215 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 17.315 r_dihedral_angle_1_deg 5.463 r_angle_refined_deg 1.751 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.215 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 17.315 r_dihedral_angle_1_deg 5.463 r_angle_refined_deg 1.751 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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_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 1258 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing