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Crystal structure of variable lymphocyte receptor VLRA.R5.1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M18 PDB ENTRY 3M18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 20% (w/v) polyethylene glycol 6000, 1.0 M LiCl and 0.1 M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.333 α = 90 b = 77.053 β = 112.04 c = 65.392 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 300 mm CCD 2009-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.7 50 0.101 12.9 3.7 48278 16.9
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) 1.7 1.82 0.322 2.5 2.9
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 3M18 1.7 50 48278 2561 99.78 0.21175 0.20944 0.2079 0.25494 0.2535 RANDOM 25.207
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] -1.31 -0.65 2.23 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.583 r_dihedral_angle_4_deg 14.721 r_dihedral_angle_3_deg 14.205 r_dihedral_angle_1_deg 6.116 r_scangle_it 4.775 r_scbond_it 3.045 r_mcangle_it 1.787 r_angle_refined_deg 1.626 r_mcbond_it 1.135 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.583 r_dihedral_angle_4_deg 14.721 r_dihedral_angle_3_deg 14.205 r_dihedral_angle_1_deg 6.116 r_scangle_it 4.775 r_scbond_it 3.045 r_mcangle_it 1.787 r_angle_refined_deg 1.626 r_mcbond_it 1.135 r_nbtor_refined 0.314 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 3632 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling