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Structure of new antigen receptor variable domain from sharks
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VER PDB ENTRY 1VER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 298 0.1M Chess PH9.5, 50% PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.1 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.268 α = 90 b = 68.324 β = 90 c = 39.511 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 315 RH COATED SI MIRROR 2004-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 34.2 98.55 0.126 15.2 7.2 6336 35.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 100 0.977 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 (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 1VER 2.1 34.2 6336 6336 289 98.55 0.22042 0.22042 0.21753 0.2187 0.28048 0.2813 RANDOM 49.94
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] -2.3 2.14 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.342 r_dihedral_angle_3_deg 17.825 r_dihedral_angle_4_deg 13.958 r_dihedral_angle_1_deg 7.26 r_scangle_it 2.443 r_scbond_it 1.564 r_angle_refined_deg 1.494 r_mcangle_it 0.911 r_mcbond_it 0.527 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.342 r_dihedral_angle_3_deg 17.825 r_dihedral_angle_4_deg 13.958 r_dihedral_angle_1_deg 7.26 r_scangle_it 2.443 r_scbond_it 1.564 r_angle_refined_deg 1.494 r_mcangle_it 0.911 r_mcbond_it 0.527 r_nbtor_refined 0.307 r_nbd_refined 0.266 r_symmetry_hbond_refined 0.246 r_xyhbond_nbd_refined 0.232 r_symmetry_vdw_refined 0.21 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 823 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CCP4 model building REFMAC refinement MOLREP phasing