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Listeria monocytogene InlB (internalin B) residues 36-392 (internalin domain and B-repeat)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H6T 1H6T, 2Y5P experimental model PDB 2Y5P 1H6T, 2Y5P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Reservoir solution (Morpheus screen (Molecular Dimensions) condition E6): 0.1 M (HEPES sodium salt / MOPS acid), pH 7.5, 20 % v/v ethylene glycol, 10 % w/v PEG 8,000, 0.03 M diethylene glycol, 0.03 M triethylene-glycol, 0.03 M tetraethylene glycol, 0.03 M pentaethylene glycol;
Protein solution: 10 mg/ml in 10 mM Tris, pH 8.0, 20 mM NaCl;
Drop size: 100 nl + 100 nl (protein + reservoir)
Crystal Properties Matthews coefficient Solvent content 3 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.49 α = 90 b = 148.41 β = 90 c = 220.02 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 6M 2017-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9164 PETRA III, EMBL c/o DESY P13 (MX1)
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 3.3 50 99.9 0.34 0.992 6.49 8.5 22938 56.76
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 3.3 3.39 99.9 1.205 0.6 1.96 8.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1H6T, 2Y5P 3.3 48.27 1.34 22824 1112 99.7 0.2324 0.2303 0.2339 0.2723 0.2759 61.47
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 11.9956 f_angle_d 0.6313 f_chiral_restr 0.0492 f_plane_restr 0.0046 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8279 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing