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Crystal structure of a dimeric inhibited of peptidyl tRNA hydrolase at 1.76A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100mM HEPES, 20% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.51 51.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.56 α = 90 b = 98.33 β = 90 c = 123.93 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 CCD MARMOSAIC 225 mm CCD 2019-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97 RRCAT INDUS-2 PX-BL21
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 1.76 45.74 98 0.13 0.14 0.058 0.991 8.4 6.2 42085
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.8 95 0.47 0.51 0.2 0.84 2.9 5.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5YN4 1.76 45.74 42085 2063 98.002 0.184 0.1826 0.1942 0.2184 0.2291 14.094
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] 0.07 -0.577 0.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.382 r_dihedral_angle_3_deg 13.923 r_dihedral_angle_4_deg 13.746 r_dihedral_angle_1_deg 6.359 r_lrange_it 6.265 r_lrange_other 5.945 r_scangle_it 3.421 r_scangle_other 3.421 r_mcangle_it 2.43 r_mcangle_other 2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.382 r_dihedral_angle_3_deg 13.923 r_dihedral_angle_4_deg 13.746 r_dihedral_angle_1_deg 6.359 r_lrange_it 6.265 r_lrange_other 5.945 r_scangle_it 3.421 r_scangle_other 3.421 r_mcangle_it 2.43 r_mcangle_other 2.43 r_scbond_it 2.179 r_scbond_other 2.178 r_angle_refined_deg 1.617 r_mcbond_other 1.486 r_mcbond_it 1.485 r_angle_other_deg 1.482 r_symmetry_nbd_refined 0.314 r_symmetry_xyhbond_nbd_other 0.285 r_nbd_other 0.263 r_xyhbond_nbd_refined 0.238 r_nbd_refined 0.217 r_symmetry_nbd_other 0.193 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.162 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2952 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing