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Listeria monocytogenes internalin-like protein lmo2027
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 300 Protein: 12.6 mg/ml, 0.5 M NaCl, 10 mM Tris pH 8.3, 1 mM TCEP
Crystallization condition: Classics II D4 (Qiagen),
0.1 M Citric acid (pH 3.5) and 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.95 58.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.776 α = 90 b = 157.776 β = 90 c = 36.28 γ = 90
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 2016-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.978 APS 21-ID-F
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 2.3 30 98.6 0.09 16.6 6.2 20009
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 99.6 0.571 0.881 1.9 4.5
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 5HL3 2.3 30 19031 974 98.43 0.23031 0.22784 0.2245 0.27907 0.2763 RANDOM 84.536
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] -4.28 -4.28 8.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.09 r_dihedral_angle_3_deg 15.979 r_dihedral_angle_4_deg 14.888 r_dihedral_angle_1_deg 6.57 r_long_range_B_refined 5.028 r_long_range_B_other 5.027 r_scangle_other 2.961 r_mcangle_it 2.847 r_mcangle_other 2.846 r_scbond_it 1.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.09 r_dihedral_angle_3_deg 15.979 r_dihedral_angle_4_deg 14.888 r_dihedral_angle_1_deg 6.57 r_long_range_B_refined 5.028 r_long_range_B_other 5.027 r_scangle_other 2.961 r_mcangle_it 2.847 r_mcangle_other 2.846 r_scbond_it 1.836 r_scbond_other 1.836 r_mcbond_it 1.719 r_mcbond_other 1.719 r_angle_refined_deg 1.469 r_angle_other_deg 0.956 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2621 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing