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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 1VER 12Y-1 VNAR PDB ENTRY 1VER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.1M Sodium citrate, 20% v/v iso-Propanol, 20% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.94 58.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.283 α = 90 b = 92.046 β = 90 c = 98.224 γ = 90
Symmetry Space Group I 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 2003-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 2.18 18.12 100 0.054 0.054 32.5 6.6 14981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.24 99.4 4 6.3
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-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 12Y-1 VNAR PDB ENTRY 1VER 2.18 18.12 14981 783 99.87 0.17912 0.17912 0.17574 0.1813 0.24721 0.2534 RANDOM 21.292
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] -1.07 0.07 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.648 r_scangle_it 3.05 r_scbond_it 1.826 r_angle_refined_deg 1.484 r_mcangle_it 1.14 r_angle_other_deg 0.868 r_mcbond_it 0.591 r_nbd_other 0.251 r_symmetry_vdw_other 0.251 r_symmetry_vdw_refined 0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.648 r_scangle_it 3.05 r_scbond_it 1.826 r_angle_refined_deg 1.484 r_mcangle_it 1.14 r_angle_other_deg 0.868 r_mcbond_it 0.591 r_nbd_other 0.251 r_symmetry_vdw_other 0.251 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.199 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.101 r_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 1762 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CCP4 model building REFMAC refinement MOLREP phasing