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The crystal structure of Thioflavin-T (ThT) binding OspA mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OY7 PDB entry 2OY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 40% PEG-400, 2% glycerol, 0.85M Tris-Cl, 0.25M (NH4)2SO4, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.073 α = 90 b = 35.876 β = 105.85 c = 92.606 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 2008-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.9793 APS 23-ID-D
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 1.75 50 100 0.087 3.6 34301
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 1.75 1.81 100 0.663 1.74 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2OY7 1.75 20 30820 30820 3435 99.77 0.22808 0.22311 0.2299 0.27388 0.2806 RANDOM 9.558
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] 4.24 -0.11 -2.1 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.954 r_dihedral_angle_4_deg 22 r_dihedral_angle_3_deg 17.404 r_dihedral_angle_1_deg 5.97 r_scangle_it 3.379 r_scbond_it 2.438 r_angle_other_deg 2.277 r_angle_refined_deg 1.504 r_mcbond_it 1.233 r_mcangle_it 1.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.954 r_dihedral_angle_4_deg 22 r_dihedral_angle_3_deg 17.404 r_dihedral_angle_1_deg 5.97 r_scangle_it 3.379 r_scbond_it 2.438 r_angle_other_deg 2.277 r_angle_refined_deg 1.504 r_mcbond_it 1.233 r_mcangle_it 1.096 r_symmetry_vdw_refined 0.233 r_symmetry_vdw_other 0.22 r_nbd_other 0.216 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.173 r_mcbond_other 0.101 r_nbtor_other 0.094 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2394 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 26
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling