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Crystal structure analysis of the nurse shark New antigen Receptor PBLA8 variable domain in complex with lysozyme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 38% PEG 400, 0.1M Tris, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.96 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.979 α = 90 b = 82.719 β = 90 c = 107.363 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 CCD MARMOSAIC 325 mm CCD 2005-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.95369 SSRL BL9-2
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 1.8 33.71 98.2 0.064 19.7 4.2 60320 60320 -3 28.3
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 1.8 1.85 100 0.535 1.7 4.1 4524
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 33.71 57232 57232 3041 100 0.18664 0.18532 0.1927 0.21083 0.2142 RANDOM 31.297
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] 0.63 -0.69 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.627 r_dihedral_angle_4_deg 15.69 r_dihedral_angle_3_deg 12.79 r_dihedral_angle_1_deg 6.379 r_scangle_it 3.922 r_scbond_it 2.808 r_angle_refined_deg 1.762 r_mcangle_it 1.687 r_mcbond_it 1.398 r_angle_other_deg 1.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.627 r_dihedral_angle_4_deg 15.69 r_dihedral_angle_3_deg 12.79 r_dihedral_angle_1_deg 6.379 r_scangle_it 3.922 r_scbond_it 2.808 r_angle_refined_deg 1.762 r_mcangle_it 1.687 r_mcbond_it 1.398 r_angle_other_deg 1.006 r_mcbond_other 0.364 r_symmetry_vdw_other 0.244 r_nbd_other 0.216 r_nbd_refined 0.215 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.11 r_nbtor_other 0.089 r_symmetry_vdw_refined 0.074 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3784 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection AMoRE phasing