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Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O6R PDB ENTRY 2O6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 2.0-2.4 M NaH2PO4/K2HPO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.64 53.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.109 α = 90 b = 61.057 β = 107.35 c = 98.081 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 MarUSA MarMosaic -325 Flat Mirror 2007-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2
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 2.1 50 91.3 0.115 9 3.1 43844
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 2.1 2.18 81.3 0.293 3 2.8 3847
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 2O6R 2.1 50 41594 2232 91.06 0.22 0.217 0.2242 0.264 0.2714 RANDOM 20.107
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] 3.91 -0.36 -1.39 -2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.543 r_dihedral_angle_4_deg 23.63 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_1_deg 6.324 r_scangle_it 5.945 r_scbond_it 4.526 r_mcangle_it 2.272 r_angle_refined_deg 1.654 r_mcbond_it 1.54 r_angle_other_deg 1.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.543 r_dihedral_angle_4_deg 23.63 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_1_deg 6.324 r_scangle_it 5.945 r_scbond_it 4.526 r_mcangle_it 2.272 r_angle_refined_deg 1.654 r_mcbond_it 1.54 r_angle_other_deg 1.068 r_mcbond_other 0.313 r_symmetry_vdw_other 0.309 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.21 r_nbd_other 0.21 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.181 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.096 r_nbtor_other 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5456 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction HKL-2000 data reduction HKL-2000 data scaling CaspR phasing