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High resolution structure of lectin-like Ox-LDL receptor 1 in space group P 32 2 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 2M ammonium sulfate, 0.2 M sodium chloride, 0.1M sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.03 α = 90 b = 50.03 β = 90 c = 91.6 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 100 PIXEL DECTRIS PILATUS 6M 2020-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.257 43.33 99.5 0.098 0.101 0.025 0.998 15.4 16.7 36626
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 1.257 1.28 96.6 1.641 1.692 0.405 0.702 16.9
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 1YPU 1.27 43.33 33554 1741 99.65 0.1598 0.1578 0.1657 0.1972 0.2022 RANDOM 19.071
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] -0.38 -0.19 -0.38 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.938 r_dihedral_angle_3_deg 10.262 r_dihedral_angle_1_deg 6.146 r_dihedral_angle_4_deg 4.464 r_rigid_bond_restr 2.768 r_angle_refined_deg 1.674 r_angle_other_deg 1.174 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.938 r_dihedral_angle_3_deg 10.262 r_dihedral_angle_1_deg 6.146 r_dihedral_angle_4_deg 4.464 r_rigid_bond_restr 2.768 r_angle_refined_deg 1.674 r_angle_other_deg 1.174 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1026 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing