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PCSK9-deltaC D374A mutant bound to WT EGF-A of LDLR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W2N PDB ENTRY 2W2N
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 = 84.106 α = 90 b = 84.106 β = 90 c = 209.745 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 2008-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 98.9 0.1 10.4 4.9 23184 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 99.7 0.67 10.4 4.6
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 2W2N 2.62 40 21932 1185 98.45 0.22803 0.22589 0.2251 0.2702 0.2675 RANDOM 28.958
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] 1.88 1.88 -3.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.933 r_dihedral_angle_4_deg 18.12 r_dihedral_angle_3_deg 17.182 r_dihedral_angle_1_deg 5.268 r_scangle_it 1.439 r_angle_refined_deg 1.148 r_scbond_it 0.817 r_mcangle_it 0.658 r_mcbond_it 0.355 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.933 r_dihedral_angle_4_deg 18.12 r_dihedral_angle_3_deg 17.182 r_dihedral_angle_1_deg 5.268 r_scangle_it 1.439 r_angle_refined_deg 1.148 r_scbond_it 0.817 r_mcangle_it 0.658 r_mcbond_it 0.355 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.072 r_bond_refined_d 0.007 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 3127 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing