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Structure of new antigen receptor variable domain from sharks
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VES PDB ENTRY 1VES
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.1M ACETATE, 20% PEP (17/8 PO/OH), pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.66 66.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.498 α = 90 b = 88.661 β = 90 c = 101.754 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 113 IMAGE PLATE MAR scanner 180 mm plate AXCO MICROCAPILLARY FOCUSING OPTICS 2004-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 21.57 95.3 0.0119 0.0119 7.6 2.7 19373 56.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 87.6 0.6 0.6 1.2 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1VES 2.71 21.57 17386 17386 1969 94.8 0.189 0.18 0.1812 0.27 0.2636 RANDOM 62.12
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] 0.09 0.37 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.866 r_dihedral_angle_4_deg 20.413 r_dihedral_angle_3_deg 20.273 r_dihedral_angle_1_deg 6.983 r_scangle_it 3.085 r_scbond_it 1.837 r_angle_refined_deg 1.547 r_mcangle_it 1.185 r_mcbond_it 0.644 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.866 r_dihedral_angle_4_deg 20.413 r_dihedral_angle_3_deg 20.273 r_dihedral_angle_1_deg 6.983 r_scangle_it 3.085 r_scbond_it 1.837 r_angle_refined_deg 1.547 r_mcangle_it 1.185 r_mcbond_it 0.644 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.212 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3316 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling