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PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QTW PDB ENTRY 2QTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M HEPES PH 7.5, 10% (W/V) PEG 8000 AND 8% (V/V) ETHYLENE GLYCOL
Crystal Properties Matthews coefficient Solvent content 4.1 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.948 α = 90 b = 85.948 β = 90 c = 218.329 γ = 90
Symmetry Space Group P 43 21 2
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 ADSC CCD 2008-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.62 40 99.5 0.08 14.2 4.8 25321 3.5
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 2.62 2.76 99.9 0.7 2.3 4.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2QTW 2.62 40 23984 1287 99.2 0.22843 0.22659 0.2304 0.26311 0.2644 RANDOM 48.196
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] 4.13 4.13 -8.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.504 r_dihedral_angle_4_deg 21.141 r_dihedral_angle_3_deg 18.119 r_dihedral_angle_1_deg 5.969 r_scangle_it 1.492 r_angle_refined_deg 1.238 r_scbond_it 0.892 r_mcangle_it 0.734 r_mcbond_it 0.401 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.504 r_dihedral_angle_4_deg 21.141 r_dihedral_angle_3_deg 18.119 r_dihedral_angle_1_deg 5.969 r_scangle_it 1.492 r_angle_refined_deg 1.238 r_scbond_it 0.892 r_mcangle_it 0.734 r_mcbond_it 0.401 r_nbtor_refined 0.301 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.2 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3125 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing