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Crystal structure of variable lymphocyte receptor VLRA.R2.1 in complex with hen egg lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E6J PDB ENTRY 3E6J PDB ENTRY 2VB1 experimental model PDB 2VB1 PDB ENTRY 3E6J PDB ENTRY 2VB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 15% (w/v) polyethylene glycol 2000 and 0.1 M Bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.794 α = 90 b = 68.116 β = 110.94 c = 59.751 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 ADSC QUANTUM 315 2008-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0 NSLS X29A
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 1.95 55.815 0.087 33.2 6.4 24789 28.3
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) 1.95 2.02 80.2 0.34 3.2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3E6J
PDB ENTRY 2VB1 1.95 55.81 23522 1249 96.76 0.18425 0.18121 0.1803 0.23989 0.2387 RANDOM 29.771
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] 0.55 1.02 1.09 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.608 r_dihedral_angle_4_deg 19.322 r_dihedral_angle_3_deg 14.246 r_dihedral_angle_1_deg 6.343 r_scangle_it 4.441 r_scbond_it 2.768 r_mcangle_it 1.591 r_angle_refined_deg 1.58 r_mcbond_it 0.991 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.608 r_dihedral_angle_4_deg 19.322 r_dihedral_angle_3_deg 14.246 r_dihedral_angle_1_deg 6.343 r_scangle_it 4.441 r_scbond_it 2.768 r_mcangle_it 1.591 r_angle_refined_deg 1.58 r_mcbond_it 0.991 r_nbtor_refined 0.306 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_refined 0.154 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2853 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 5
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling