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Variable Lymphocyte Receptor Recognition of the Immunodominant Glycoprotein of Bacillus anthracis Spores
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R6Q PDB entries 2R6Q, 2R9U experimental model PDB 2R9U PDB entries 2R6Q, 2R9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.26 298 15% PEG 6000, 1.2 M LiCl, 0.1 M sodium citrate, pH 5.26, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.809 α = 90 b = 146.528 β = 90 c = 209.501 γ = 90
Symmetry Space Group I 2 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 100 CCD MARMOSAIC 300 mm CCD 2010-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
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 2.55 50 97.3 0.122 9.5 3.1 37042 37042 -3
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 2.55 2.64 99.1 0.581 2 2.9
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 2R6Q, 2R9U 2.55 41.88 35031 35031 1869 96.69 0.19149 0.18932 0.23293 0.2234 RANDOM 35.948
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] 0.28 -1.47 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.135 r_dihedral_angle_3_deg 12.429 r_dihedral_angle_4_deg 9.503 r_dihedral_angle_1_deg 6.406 r_angle_other_deg 4.419 r_angle_refined_deg 1.211 r_chiral_restr 0.062 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.135 r_dihedral_angle_3_deg 12.429 r_dihedral_angle_4_deg 9.503 r_dihedral_angle_1_deg 6.406 r_angle_other_deg 4.419 r_angle_refined_deg 1.211 r_chiral_restr 0.062 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6289 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling