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Lipoprotein(a) Kringle IV domain 8 - Lp(a) KIV8 in complex with LY3353871
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1000 mM trisodium citrate pH 7.0, 100 mM HEPES pH 6.0
Crystal Properties Matthews coefficient Solvent content 1.9 35.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.602 α = 90 b = 57.574 β = 94.7 c = 38.305 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 PIXEL DECTRIS PILATUS 6M 2015-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
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 1.07 18.74 91.1 0.068 7.9 3.5 61826
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 1.07 1.13 91.1 0.607 1.8 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.07 18.74 61502 3236 91.02 0.16214 0.16099 0.17 0.18291 0.1893 RANDOM 10.597
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] 0.03 -0.41 -0.59 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.381 r_dihedral_angle_4_deg 14.969 r_dihedral_angle_3_deg 12.58 r_sphericity_free 10.799 r_sphericity_bonded 6.3 r_dihedral_angle_1_deg 6.215 r_long_range_B_refined 2.037 r_scbond_it 1.868 r_angle_refined_deg 1.379 r_mcangle_it 1.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.381 r_dihedral_angle_4_deg 14.969 r_dihedral_angle_3_deg 12.58 r_sphericity_free 10.799 r_sphericity_bonded 6.3 r_dihedral_angle_1_deg 6.215 r_long_range_B_refined 2.037 r_scbond_it 1.868 r_angle_refined_deg 1.379 r_mcangle_it 1.332 r_mcbond_it 1.207 r_rigid_bond_restr 0.959 r_chiral_restr 0.09 r_bond_refined_d 0.009 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1431 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing