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Structure of New Antigen Receptor variable domain from sharks
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M BIS-TRIS PROPANE, 45% PPG P400, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.14 60.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.259 α = 90 b = 97.259 β = 90 c = 65.228 γ = 90
Symmetry Space Group I 41 2 2
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 2003-10-18 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 2.82 69.01 99 0.045 0.045 18.1 15.1 3975
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 2.82 2.9 94.3 1.8 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 2.82 6 3353 153 99.29 0.16972 0.16972 0.16588 0.1749 0.25391 0.2662 RANDOM 40.21
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] 3.53 3.53 -7.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.873 r_scangle_it 1.864 r_angle_refined_deg 1.552 r_scbond_it 1.038 r_angle_other_deg 0.838 r_mcangle_it 0.69 r_symmetry_vdw_refined 0.37 r_symmetry_vdw_other 0.364 r_mcbond_it 0.363 r_nbd_other 0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.873 r_scangle_it 1.864 r_angle_refined_deg 1.552 r_scbond_it 1.038 r_angle_other_deg 0.838 r_mcangle_it 0.69 r_symmetry_vdw_refined 0.37 r_symmetry_vdw_other 0.364 r_mcbond_it 0.363 r_nbd_other 0.224 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.22 r_symmetry_hbond_refined 0.16 r_nbtor_other 0.089 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 770 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing REFMAC refinement