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Short PCSK9 delta-P' complex with shrunken peptide bearing homo-Arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 292 calcium acetate, PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.387 α = 90 b = 70.387 β = 90 c = 156.983 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS 6M 2017-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 50.01 100 0.111 16.1 9.9 23637 -3 32.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 97.2 0.863 2.5 9.3
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 4NMX 2.2 50.01 22615 981 99.92 0.19702 0.19537 0.23703 0.2024 RANDOM 33.642
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] -0.8 -0.4 -0.8 2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.764 r_dihedral_angle_4_deg 15.05 r_dihedral_angle_3_deg 13.245 r_long_range_B_refined 7.907 r_long_range_B_other 7.897 r_scangle_other 6.498 r_dihedral_angle_1_deg 5.9 r_mcangle_it 4.551 r_mcangle_other 4.55 r_scbond_it 4.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.764 r_dihedral_angle_4_deg 15.05 r_dihedral_angle_3_deg 13.245 r_long_range_B_refined 7.907 r_long_range_B_other 7.897 r_scangle_other 6.498 r_dihedral_angle_1_deg 5.9 r_mcangle_it 4.551 r_mcangle_other 4.55 r_scbond_it 4.157 r_scbond_other 4.156 r_mcbond_it 3.164 r_mcbond_other 3.126 r_angle_refined_deg 1.26 r_angle_other_deg 0.959 r_chiral_restr 0.065 r_gen_planes_refined 0.021 r_gen_planes_other 0.017 r_bond_refined_d 0.008 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2869 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing