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Crystal structure of peptidyl-tRNA hydrolase from Enterococcus faecium at 1.22 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Y52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.2M Ammonium Sulphate, 0.1M Tris-HCl pH 7.5, 15% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.82 32.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.765 α = 90 b = 47.584 β = 90 c = 69.168 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 CdTe 16M 2023-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.885 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.22 47.58 88.7 0.997 13.4 4.3 40928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.22 1.24 0.71
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-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 1.22 30.06 38903 1981 88.2 0.16019 0.15838 0.1584 0.19805 0.1981 RANDOM 18.027
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] 1.51 -1 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.814 r_long_range_B_refined 12.346 r_long_range_B_other 12.015 r_scangle_other 9.576 r_dihedral_angle_2_deg 8.422 r_scbond_it 7.225 r_scbond_other 7.014 r_mcangle_other 6.396 r_mcangle_it 6.393 r_dihedral_angle_1_deg 6.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.814 r_long_range_B_refined 12.346 r_long_range_B_other 12.015 r_scangle_other 9.576 r_dihedral_angle_2_deg 8.422 r_scbond_it 7.225 r_scbond_other 7.014 r_mcangle_other 6.396 r_mcangle_it 6.393 r_dihedral_angle_1_deg 6.082 r_mcbond_it 4.62 r_mcbond_other 4.615 r_rigid_bond_restr 3.733 r_angle_refined_deg 1.657 r_angle_other_deg 0.58 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1464 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing