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Crystal structure of Mycobacterium tuberculosis HtrA1 (Rv1223) in regulated conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y8T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 0.1M HEPES, 1.4M Sodium Citrate tribasic dihydrate pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.114 α = 90 b = 107.114 β = 90 c = 61.529 γ = 120
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 PILATUS3 2M CRL 2018-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9660 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.82 37.04 99.69 0.09 0.115 0.071 0.996 8.5 4.6 23356 29.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.89 96.8 0.729 0.517 1.2 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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1Y8T 1.83 37.04 23202 1119 0.191 0.227 0.2311 RANDOM 34
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] -0.77 -0.39 -0.77 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.338 r_dihedral_angle_3_deg 14.589 r_dihedral_angle_4_deg 12.211 r_dihedral_angle_1_deg 7.121 r_long_range_B_refined 5.812 r_long_range_B_other 5.811 r_scangle_other 4.257 r_mcangle_it 3.464 r_mcangle_other 3.463 r_scbond_it 2.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.338 r_dihedral_angle_3_deg 14.589 r_dihedral_angle_4_deg 12.211 r_dihedral_angle_1_deg 7.121 r_long_range_B_refined 5.812 r_long_range_B_other 5.811 r_scangle_other 4.257 r_mcangle_it 3.464 r_mcangle_other 3.463 r_scbond_it 2.925 r_scbond_other 2.924 r_mcbond_it 2.382 r_mcbond_other 2.381 r_angle_refined_deg 1.359 r_angle_other_deg 0.469 r_chiral_restr 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 2084 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing