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The 1.8 angstrom crystal structure of Yersinia pestis CO92 trehalose-6-phosphate hydrolase (TreC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A5P8YJY7-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M amino acids mix, 0.1 M buffer system 1 (Imidazole, MES monohydrate (acid)), 30% v/v precipitant mix 1 (40% v/v PEG 500* MME; 20% w/v PEG 20000).
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.661 α = 90 b = 78.737 β = 90 c = 111.102 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 EIGER2 X 9M 2023-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.8 49.55 97.1 0.138 0.176 5.9 4 50822
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 1.8 1.86 0.944 0.552 1.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1.8 49.55 50700 2378 96.58 0.192 0.1955 0.2249 0.2255 RANDOM 15.478
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] 0.82 -0.98 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.792 r_dihedral_angle_1_deg 6.231 r_scangle_it 3.007 r_scangle_other 3.004 r_mcangle_it 2.342 r_mcangle_other 2.342 r_scbond_it 1.816 r_scbond_other 1.816 r_mcbond_it 1.376 r_mcbond_other 1.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.792 r_dihedral_angle_1_deg 6.231 r_scangle_it 3.007 r_scangle_other 3.004 r_mcangle_it 2.342 r_mcangle_other 2.342 r_scbond_it 1.816 r_scbond_other 1.816 r_mcbond_it 1.376 r_mcbond_other 1.376 r_angle_refined_deg 1.025 r_angle_other_deg 0.407 r_nbd_refined 0.204 r_nbtor_refined 0.179 r_nbd_other 0.146 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.049 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4512 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing