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Recognition of the BG-H Antigen by a Lamprey Variable Lymphocyte Receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E6J PDB ENTRY 3E6J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 28.5% (w/v) PEG 3350, 0.6 M NaCl, and 0.1M Tris-HCl (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.71 α = 72.03 b = 62.784 β = 71.39 c = 63.366 γ = 84.35
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2012-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.698 59.72 93.3 88598 82662
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 1.698 1.76 87.8
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 3E6J 1.698 59.72 88598 82662 4154 93.38 0.20772 0.20566 0.20566 0.2009 0.24661 0.2409 RANDOM 22.4
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] -0.24 0.24 -0.05 0.58 -0.35 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.661 r_dihedral_angle_4_deg 19.589 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_1_deg 6.675 r_scangle_it 6.276 r_scbond_it 4.004 r_mcangle_it 2.558 r_angle_refined_deg 2.22 r_mcbond_it 1.482 r_chiral_restr 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.661 r_dihedral_angle_4_deg 19.589 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_1_deg 6.675 r_scangle_it 6.276 r_scbond_it 4.004 r_mcangle_it 2.558 r_angle_refined_deg 2.22 r_mcbond_it 1.482 r_chiral_restr 0.165 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 6642 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 48
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling