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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 1SQ2 PDB entry 1SQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 15% PEG 10,000, 0.1M imidazole malate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.79 α = 90 b = 113.81 β = 90 c = 58.44 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 1.7 46.1 96.5 0.09 14.1 4.5 54344 54344 -3 12
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) 1.7 1.73 97.7 0.497 2.3 4.5 2730
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 (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 PDB entry 1SQ2 1.7 46.1 51760 51760 2559 96.33 0.19527 0.19527 0.19402 0.2065 0.22076 0.2082 RANDOM 10.691
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] 0.33 -0.02 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.042 r_dihedral_angle_4_deg 20.243 r_dihedral_angle_3_deg 12.131 r_dihedral_angle_1_deg 6.416 r_scangle_it 4.063 r_scbond_it 3.024 r_angle_refined_deg 1.867 r_mcangle_it 1.815 r_mcbond_it 1.51 r_angle_other_deg 0.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.042 r_dihedral_angle_4_deg 20.243 r_dihedral_angle_3_deg 12.131 r_dihedral_angle_1_deg 6.416 r_scangle_it 4.063 r_scbond_it 3.024 r_angle_refined_deg 1.867 r_mcangle_it 1.815 r_mcbond_it 1.51 r_angle_other_deg 0.979 r_mcbond_other 0.374 r_symmetry_vdw_other 0.234 r_nbd_refined 0.224 r_nbd_other 0.199 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.127 r_symmetry_hbond_refined 0.093 r_nbtor_other 0.085 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3670 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing