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WT PCSK9-deltaC bound to EGF-A H306Y mutant 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, 8% (V/V) ETHYLENE GLYCOL.
Crystal Properties Matthews coefficient Solvent content 4.02 69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.94 α = 90 b = 83.94 β = 90 c = 209.933 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 2008-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.3 45 98.1 0.15 11.7 7 33566 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 2.3 2.42 99.7 0.64 2.9 7
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 2.3 40 31695 1691 97.41 0.21531 0.21332 0.2154 0.25393 0.2513 RANDOM 22.177
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] 1.49 1.49 -2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.844 r_dihedral_angle_3_deg 15.347 r_dihedral_angle_4_deg 14.361 r_dihedral_angle_1_deg 7.002 r_scangle_it 1.561 r_angle_refined_deg 1.188 r_angle_other_deg 1.028 r_scbond_it 1.002 r_mcangle_it 0.759 r_mcbond_it 0.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.844 r_dihedral_angle_3_deg 15.347 r_dihedral_angle_4_deg 14.361 r_dihedral_angle_1_deg 7.002 r_scangle_it 1.561 r_angle_refined_deg 1.188 r_angle_other_deg 1.028 r_scbond_it 1.002 r_mcangle_it 0.759 r_mcbond_it 0.437 r_symmetry_hbond_refined 0.286 r_symmetry_vdw_other 0.248 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.186 r_nbd_other 0.183 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.099 r_nbtor_other 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 3132 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing