☰ Navigation Tabs
Vaccinia L1/M12B9-Fab complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YPY 1YPY,1SY6 experimental model PDB 1SY6 1YPY,1SY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Initial crystallization experiments were carried out by sitting-drop vapor diffusion in a 96-well format, using a Phoenix liquid-handling robot with a panel of commercial sparse-matrix screens (PEG/Ion 1 and 2 from Hampton Research, Wizard 2 from Emerald Biosciences, JCSG Plus Suite from Qiagen, and JBScreen 6 from Jena BioScience). Quality diffracting crystals of L1/M12B9-Fab complex were obtained at RT by mixing 0.5ul of protein solution at 9.5 mg/ml with 0.5ul of precipitant [100 mM Tris, pH 7.0, 20% (w/v) polyethylene glycol (PEG) 3000, and 200 mM Ca(OAc)] and seeding with initial crystals obtained at 6.5 mg/ml. Crystal were flash-frozen at 100K in mother liquor containing 20 % glycerol.
Crystal Properties Matthews coefficient Solvent content 2.6 52.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.829 α = 90 b = 102.829 β = 90 c = 238.355 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS 6M 2013-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.1 47.67 99.9 0.2 0.077 9.7 9.2 27308 1.7
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 FREE R-VALUE 1YPY,1SY6 3.1 47.21 25898 1367 99.9 0.21221 0.20938 0.2111 0.26491 0.267 RANDOM 64.52
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.017 r_dihedral_angle_4_deg 14.581 r_dihedral_angle_3_deg 12.955 r_dihedral_angle_1_deg 4.964 r_angle_refined_deg 0.865 r_angle_other_deg 0.644 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.017 r_dihedral_angle_4_deg 14.581 r_dihedral_angle_3_deg 12.955 r_dihedral_angle_1_deg 4.964 r_angle_refined_deg 0.865 r_angle_other_deg 0.644 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9188 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement