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Structure of a lamprey variable lymphocyte receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O6S PDB ENTRY 2O6S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 296 70% (w/v) 2-methyl-2,4-pentanediol and 0.1 M Hepes, pH 7.5, EVAPORATION, temperature 296K
Crystal Properties Matthews coefficient Solvent content 1.88 34.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.543 α = 90 b = 49.543 β = 90 c = 97.912 γ = 120
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 2008-07-01 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 1.55 30 0.058 55.8 22.2 19434 19.9
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) 1.55 1.61 0.446 6.9 20 1908
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 2O6S 1.55 30 18422 998 98.53 0.16454 0.16263 0.1705 0.19921 0.2059 RANDOM 19.684
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] 0.39 0.19 0.39 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.342 r_dihedral_angle_4_deg 23.848 r_dihedral_angle_3_deg 14.051 r_dihedral_angle_1_deg 6.05 r_scangle_it 4.465 r_scbond_it 3.03 r_mcangle_it 2.069 r_angle_refined_deg 1.79 r_mcbond_it 1.207 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.342 r_dihedral_angle_4_deg 23.848 r_dihedral_angle_3_deg 14.051 r_dihedral_angle_1_deg 6.05 r_scangle_it 4.465 r_scbond_it 3.03 r_mcangle_it 2.069 r_angle_refined_deg 1.79 r_mcbond_it 1.207 r_nbtor_refined 0.32 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.209 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 1296 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling