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PCSK9 bound to small molecule inhibitor AZD-0780
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QTW Published PCSK9 structure, PDB 2QTW, used as molecular-replacement search model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 293.15 0.10 M MD - Buffer System 1, pH 5.80, 13.00 % MD - Precipitant Mix 2, 2.50 % (v/v) MD - Cryopolyols , 90.00 mM MD -
LiNaK Mix
Crystal Properties Matthews coefficient Solvent content 2.49 50.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.99 α = 90 b = 109.447 β = 90 c = 122.602 γ = 90
Symmetry Space Group P 21 2 21
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 EIGER2 X 16M 2025-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.91508 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.07 109.45 40.6 0.54 0.59 0.24 0.98 4.2 11.5 35755
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.45 5.2 1.67 1.83 0.74 0.77 1.6 11.2
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 (All) 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 2QTW 2.072 109.447 35755 1829 40.62 0.331 0.331 0.3273 0.3091 0.405 0.3805 RANDOM 35.888
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] 6.334 -10.818 4.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.273 r_dihedral_angle_6_deg 9.15 r_dihedral_angle_2_deg 6.149 r_dihedral_angle_1_deg 5.066 r_lrange_it 4.017 r_lrange_other 3.939 r_mcangle_it 1.773 r_mcangle_other 1.773 r_scangle_it 1.385 r_scangle_other 1.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.273 r_dihedral_angle_6_deg 9.15 r_dihedral_angle_2_deg 6.149 r_dihedral_angle_1_deg 5.066 r_lrange_it 4.017 r_lrange_other 3.939 r_mcangle_it 1.773 r_mcangle_other 1.773 r_scangle_it 1.385 r_scangle_other 1.385 r_mcbond_it 1.001 r_mcbond_other 1.001 r_angle_refined_deg 0.802 r_scbond_it 0.766 r_scbond_other 0.766 r_angle_other_deg 0.317 r_symmetry_nbd_refined 0.235 r_symmetry_xyhbond_nbd_refined 0.225 r_nbd_other 0.19 r_symmetry_nbd_other 0.182 r_nbd_refined 0.16 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.139 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_1 0.065 r_chiral_restr 0.037 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8277 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling STARANISO data scaling PHASER phasing