☰ Navigation Tabs
Structural basis for the binding of monoclonal antibody 5D2 to the tryptophan-rich lipid-binding loop in lipoprotein lipase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 16-22% PEG 3350, 250mM Sodium Thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.31 46.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.624 α = 90 b = 67.745 β = 94.369 c = 130.073 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 9M NULL 2019-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-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 2.74 29.264 99.29 0.12 0.133 0.057 0.995 10.4 5.1 23348
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 2.74 2.84 93.72 0.692 0.769 0.33 0.729 1.9 5.08
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5D8J 2.8 29.264 22291 1066 99.816 0.21 0.2079 0.217 0.2427 0.2487 Random selection 54.434
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] 1.721 -2.888 2.905 -4.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.766 r_dihedral_angle_4_deg 16.247 r_dihedral_angle_3_deg 15.146 r_dihedral_angle_1_deg 6.917 r_lrange_it 4.519 r_lrange_other 4.519 r_mcangle_it 1.916 r_mcangle_other 1.916 r_scangle_it 1.531 r_scangle_other 1.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.766 r_dihedral_angle_4_deg 16.247 r_dihedral_angle_3_deg 15.146 r_dihedral_angle_1_deg 6.917 r_lrange_it 4.519 r_lrange_other 4.519 r_mcangle_it 1.916 r_mcangle_other 1.916 r_scangle_it 1.531 r_scangle_other 1.531 r_angle_refined_deg 1.263 r_mcbond_it 1.076 r_mcbond_other 1.076 r_angle_other_deg 1.073 r_scbond_it 0.865 r_scbond_other 0.864 r_nbd_other 0.176 r_symmetry_nbd_other 0.165 r_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.161 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.153 r_symmetry_nbd_refined 0.143 r_ncsr_local_group_3 0.135 r_ncsr_local_group_2 0.122 r_ncsr_local_group_1 0.104 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.039 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6797 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data scaling HKL-2000 data reduction PHASER phasing