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The crystal structure of IpaH1.4 LRR domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B0N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 50 mM imidazole (pH 8.0), 1.2 M NaCl.
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.467 α = 90 b = 68.039 β = 100.72 c = 100.26 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 RAYONIX MX300HE 2017-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.4 50 98.6 0.062 33.9 3.1 86206
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 1.4 1.42 0.487 4
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 5B0N 1.4 50 80738 4265 98.22 0.18712 0.18543 0.1864 0.21984 0.2209 RANDOM 17.799
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] -0.23 -0.45 -0.23 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.476 r_dihedral_angle_4_deg 13.111 r_dihedral_angle_3_deg 12.9 r_long_range_B_refined 7.547 r_long_range_B_other 7.201 r_dihedral_angle_1_deg 6.434 r_scangle_other 5.331 r_scbond_it 3.679 r_scbond_other 3.678 r_angle_refined_deg 2.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.476 r_dihedral_angle_4_deg 13.111 r_dihedral_angle_3_deg 12.9 r_long_range_B_refined 7.547 r_long_range_B_other 7.201 r_dihedral_angle_1_deg 6.434 r_scangle_other 5.331 r_scbond_it 3.679 r_scbond_other 3.678 r_angle_refined_deg 2.502 r_mcangle_it 2.388 r_mcangle_other 2.387 r_mcbond_it 1.815 r_mcbond_other 1.815 r_angle_other_deg 1.291 r_chiral_restr 0.177 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 3621 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction