☰ Navigation Tabs
Crystal structure analysis of the nurse shark New Antigen Receptor PBLA8 variable domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SQ2 PDB ENTRY 1SQ2, CHAIN N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 24% PEG 400, 0.1M Na/K phosphate, 0.15M NaCl, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 42.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.958 α = 90 b = 53.958 β = 90 c = 79.077 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2005-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.97623 ALS 8.2.1
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 1.35 44.7 98.7 0.056 16.7 3.8 26060 26060 -3 14
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) 1.35 1.37 95.6 0.46 1.9 1.95 1226
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 1SQ2, CHAIN N 1.35 44.7 24753 24753 1253 98.71 0.1741 0.17212 0.2346 0.2143 0.2587 RANDOM 17.858
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] -0.37 -0.37 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.123 r_dihedral_angle_4_deg 16.629 r_dihedral_angle_3_deg 9.976 r_sphericity_free 9.864 r_dihedral_angle_1_deg 6.18 r_scangle_it 5.339 r_scbond_it 4.469 r_sphericity_bonded 4.061 r_mcangle_it 3.02 r_mcbond_it 2.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.123 r_dihedral_angle_4_deg 16.629 r_dihedral_angle_3_deg 9.976 r_sphericity_free 9.864 r_dihedral_angle_1_deg 6.18 r_scangle_it 5.339 r_scbond_it 4.469 r_sphericity_bonded 4.061 r_mcangle_it 3.02 r_mcbond_it 2.569 r_rigid_bond_restr 2.132 r_angle_refined_deg 1.802 r_angle_other_deg 0.998 r_mcbond_other 0.797 r_symmetry_vdw_other 0.327 r_nbd_other 0.221 r_nbd_refined 0.199 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.129 r_nbtor_other 0.085 r_symmetry_vdw_refined 0.058 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 872 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection EPMR phasing