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Crystal Structure of H. influenzae TrmD in complex with Compound 13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YVH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 20% PEG3350
0.1 M HEPES, pH 7.5
0.1 M potassium citrate tribasic
Crystal Properties Matthews coefficient Solvent content 2.65 53.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.671 α = 90 b = 94.671 β = 90 c = 177.958 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 CCD RIGAKU SATURN 944+ 2020-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.8 47.38 99.8 0.157 0.174 0.075 0.997 14.9 10.5 28700
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 1.8 1.84 1.186 1.357 0.643 0.559 7.3
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 4YVH 1.8 47.38 28698 2931 99.805 0.163 0.1613 0.1614 0.1794 0.1794 18.697
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] 0.002 0.001 0.002 -0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.577 r_dihedral_angle_3_deg 14.019 r_dihedral_angle_4_deg 11.995 r_lrange_it 11.218 r_lrange_other 10.667 r_dihedral_angle_1_deg 6.534 r_scangle_it 4.899 r_scangle_other 4.897 r_scbond_it 3.338 r_scbond_other 3.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.577 r_dihedral_angle_3_deg 14.019 r_dihedral_angle_4_deg 11.995 r_lrange_it 11.218 r_lrange_other 10.667 r_dihedral_angle_1_deg 6.534 r_scangle_it 4.899 r_scangle_other 4.897 r_scbond_it 3.338 r_scbond_other 3.319 r_mcangle_it 2.931 r_mcangle_other 2.931 r_mcbond_it 2.158 r_mcbond_other 2.147 r_angle_refined_deg 1.847 r_angle_other_deg 1.521 r_symmetry_xyhbond_nbd_refined 0.412 r_xyhbond_nbd_refined 0.33 r_nbd_other 0.252 r_nbd_refined 0.231 r_symmetry_nbd_other 0.203 r_symmetry_nbd_refined 0.189 r_nbtor_refined 0.172 r_chiral_restr 0.108 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1947 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction StructureStudio data collection PHASER phasing