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Recognition of the Thomsen-Friedenreich 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 20% (w/v) polyethylene glycol (PEG) 3350, 4% (v/v) glycerol, and 0.1M Tris-HCl (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.03 39.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.68 α = 90 b = 68.68 β = 93.58 c = 99.92 γ = 90
Symmetry Space Group P 1 21 1
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++ 2012-05-08 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 2.2 33.66 99.1 39152 38816
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 2.2 2.28 95.8
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 2.2 33.66 39152 38816 2049 99.23 0.20397 0.20129 0.20129 0.1991 0.25142 0.2491 RANDOM 28.598
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] 1.7 -0.88 -1.28 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.258 r_dihedral_angle_4_deg 19.036 r_dihedral_angle_3_deg 13.06 r_dihedral_angle_1_deg 6.121 r_scangle_it 4.563 r_scbond_it 2.82 r_mcangle_it 1.937 r_angle_refined_deg 1.657 r_mcbond_it 1.098 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.258 r_dihedral_angle_4_deg 19.036 r_dihedral_angle_3_deg 13.06 r_dihedral_angle_1_deg 6.121 r_scangle_it 4.563 r_scbond_it 2.82 r_mcangle_it 1.937 r_angle_refined_deg 1.657 r_mcbond_it 1.098 r_chiral_restr 0.1 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 6656 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 78
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement CrystalClear data reduction SCALA data scaling