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Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 in Complex with H-trisaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R9U PDB ENTRY 2R9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 295 1.9 M (NH4)2SO4, 0.1 M Sodium Citrate (pH 5.6), 0.2 M K/Na Tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.59 52.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.221 α = 90 b = 48.564 β = 116.51 c = 55.477 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 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) 2008-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1
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 1.67 50 95.3 0.089 13.8 3.6 30080 28666 -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 1.67 1.71 71.1 0.228 3.7 2.7 2120
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2R9U 1.67 49.63 28613 27202 1454 95.07 0.14825 0.1464 0.1598 0.18221 0.1908 RANDOM 11.524
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] 1.63 -0.08 -0.97 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.511 r_dihedral_angle_4_deg 20.817 r_dihedral_angle_3_deg 10.696 r_dihedral_angle_1_deg 6.131 r_scangle_it 5.569 r_scbond_it 3.648 r_mcangle_it 2.131 r_angle_refined_deg 1.62 r_angle_other_deg 1.548 r_mcbond_it 1.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.511 r_dihedral_angle_4_deg 20.817 r_dihedral_angle_3_deg 10.696 r_dihedral_angle_1_deg 6.131 r_scangle_it 5.569 r_scbond_it 3.648 r_mcangle_it 2.131 r_angle_refined_deg 1.62 r_angle_other_deg 1.548 r_mcbond_it 1.186 r_mcbond_other 0.271 r_chiral_restr 0.197 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1678 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing