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The crystal structure of IpaH2.5 LRR domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M succinic acid pH 6.6, 18.8% (w/v) polyethylene glycol (PEG)3350
Crystal Properties Matthews coefficient Solvent content 6.74 81.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.785 α = 90 b = 137.686 β = 90 c = 163.563 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 EIGER X 16M 2017-12-01 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 3.3 50 96 0.152 22 6.6 22003 56.82
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 3.301 3.419 100 0.053 4.9
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 7YA7 3.4 50 20798 1123 96.06 0.20039 0.19796 0.2004 0.24494 0.2358 RANDOM 62.278
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] -0.15 -0.29 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.837 r_long_range_B_refined 18.097 r_long_range_B_other 18.095 r_dihedral_angle_4_deg 15.578 r_scangle_other 15.548 r_mcangle_it 13.765 r_mcangle_other 13.763 r_dihedral_angle_3_deg 13.039 r_scbond_it 11.168 r_scbond_other 11.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.837 r_long_range_B_refined 18.097 r_long_range_B_other 18.095 r_dihedral_angle_4_deg 15.578 r_scangle_other 15.548 r_mcangle_it 13.765 r_mcangle_other 13.763 r_dihedral_angle_3_deg 13.039 r_scbond_it 11.168 r_scbond_other 11.166 r_mcbond_it 9.851 r_mcbond_other 9.85 r_dihedral_angle_1_deg 4.304 r_angle_refined_deg 0.677 r_angle_other_deg 0.519 r_chiral_restr 0.049 r_bond_refined_d 0.008 r_gen_planes_refined 0.001 r_bond_other_d r_gen_planes_other 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 3809 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing