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The High-Resolution Structure of a Variable Lymphocyte Receptor from Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 2.5-2.8 M ammonium sulfate, 2% hexyleneglycol, 100 mM HEPPS (pH 8)
Crystal Properties Matthews coefficient Solvent content 1.95 36.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.522 α = 90 b = 53.137 β = 90 c = 60.348 γ = 90
Symmetry Space Group P 21 21 21
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 Bruker PHOTON II 2023-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.3 40 98 0.051 20.1 8.1 36207
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.4 94 0.42 3.3 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.3 39.88 34487 1720 98.09 0.18634 0.18465 0.1926 0.22175 0.2307 RANDOM 16.335
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.445 r_dihedral_angle_4_deg 17.776 r_dihedral_angle_3_deg 14.928 r_dihedral_angle_1_deg 7.518 r_long_range_B_refined 5.597 r_long_range_B_other 5.455 r_scangle_other 3.818 r_mcangle_it 2.719 r_mcangle_other 2.718 r_scbond_it 2.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.445 r_dihedral_angle_4_deg 17.776 r_dihedral_angle_3_deg 14.928 r_dihedral_angle_1_deg 7.518 r_long_range_B_refined 5.597 r_long_range_B_other 5.455 r_scangle_other 3.818 r_mcangle_it 2.719 r_mcangle_other 2.718 r_scbond_it 2.523 r_scbond_other 2.469 r_mcbond_it 1.766 r_mcbond_other 1.762 r_angle_refined_deg 1.636 r_angle_other_deg 1.431 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1315 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing