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Crystal Structure of H. influenzae TrmD in complex with Compound 27
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 2.64 53.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.63 α = 90 b = 94.63 β = 90 c = 178.015 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 2.4 47.36 100 0.17 0.199 0.102 0.994 11.6 6.9 12287
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 2.4 2.49 0.929 1.124 0.624 0.696 5.7
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 2.4 47.36 12287 588 99.886 0.181 0.1777 0.1779 0.2526 0.2529 29.48
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] 0.104 0.052 0.104 -0.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.4 r_dihedral_angle_3_deg 17.295 r_dihedral_angle_4_deg 16.031 r_lrange_it 7.639 r_lrange_other 7.634 r_dihedral_angle_1_deg 7.431 r_scangle_it 5.864 r_scangle_other 5.862 r_mcangle_other 5.144 r_mcangle_it 5.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.4 r_dihedral_angle_3_deg 17.295 r_dihedral_angle_4_deg 16.031 r_lrange_it 7.639 r_lrange_other 7.634 r_dihedral_angle_1_deg 7.431 r_scangle_it 5.864 r_scangle_other 5.862 r_mcangle_other 5.144 r_mcangle_it 5.143 r_scbond_it 3.91 r_scbond_other 3.908 r_mcbond_it 3.479 r_mcbond_other 3.471 r_angle_refined_deg 1.898 r_angle_other_deg 1.392 r_symmetry_xyhbond_nbd_refined 0.445 r_nbd_other 0.219 r_nbd_refined 0.216 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.12 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1947 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction StructureStudio data collection PHASER phasing