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Crystal Structure Analysis of the Nurse Shark New Antigen Receptor (NAR) Variable Domain in Complex With Lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LKS PDB ENTRIES 1LKS AND 1QLE (residues 1-85) experimental model PDB 1QLE PDB ENTRIES 1LKS AND 1QLE (residues 1-85)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 15% PEG 10,000, 0.1M imidazole HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.02 α = 90 b = 109.84 β = 90 c = 29.28 γ = 90
Symmetry Space Group P 21 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 2004-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 ALS 8.3.1
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 1.45 35 93.1 0.054 37.9 4.6 40482 40482 -3 17
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 1.45 1.48 52.6 0.394 2
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 ENTRIES 1LKS AND 1QLE (residues 1-85) 1.45 35 40410 40410 2025 93.16 0.19744 0.19601 0.2046 0.22534 0.2288 RANDOM 16.334
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] -0.1 -0.31 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_4_deg 17.499 r_dihedral_angle_3_deg 12.588 r_dihedral_angle_1_deg 6.097 r_scangle_it 3.835 r_scbond_it 2.875 r_mcangle_it 1.957 r_angle_refined_deg 1.724 r_mcbond_it 1.615 r_angle_other_deg 0.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_4_deg 17.499 r_dihedral_angle_3_deg 12.588 r_dihedral_angle_1_deg 6.097 r_scangle_it 3.835 r_scbond_it 2.875 r_mcangle_it 1.957 r_angle_refined_deg 1.724 r_mcbond_it 1.615 r_angle_other_deg 0.938 r_mcbond_other 0.356 r_symmetry_vdw_other 0.255 r_nbd_refined 0.229 r_nbd_other 0.2 r_symmetry_hbond_refined 0.183 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.123 r_nbtor_other 0.084 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1835 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing