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InlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (internalin B) residues 36-392
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H6T experimental model PDB 2Y5P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 Reservoir solution: MORPHEUS Screen, Condition F3: 0.1 M mixture of imidazole and MES (acid) pH 6.5, 10% PEG4000, 20% glycerol, 0.02 M of each monosaccaharide: D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine.
Protein buffer: 10 mM Tris pH 8.0, 20 mM NaCl.
Protein concentration: 10 mg/ml.
Drop size: 1 ul protein + 1 ul reservoir.
Crystal Properties Matthews coefficient Solvent content 3.05 59.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.92 α = 90 b = 149.17 β = 90 c = 220.81 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2018-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.6 50 98 0.072 0.999 19.04 13.33 192399 24.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 96.4 1.592 0.627 2 12.46
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 20.13 1.34 192170 9649 97.97 0.174 0.1728 0.1737 0.1959 0.1967 37.79
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.0508 f_angle_d 0.8653 f_chiral_restr 0.0583 f_bond_d 0.0084 f_plane_restr 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8483 Nucleic Acid Atoms Solvent Atoms 1405 Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing