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Crystal Structure of H. influenzae TrmD in complex with Compound 30
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 2.61 52.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.367 α = 90 b = 94.367 β = 90 c = 178.289 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+ 2020-09-25 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 47.228 99.8 0.07 0.078 0.033 0.999 26.1 10.4 28538
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 0.019 0.021 0.01 0.999 8.2
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 47.228 28536 2754 99.658 0.171 0.1677 0.1677 0.2027 0.203 25.033
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.476 r_dihedral_angle_3_deg 14.87 r_dihedral_angle_4_deg 12.605 r_lrange_it 8.979 r_lrange_other 8.779 r_scangle_it 7.212 r_scangle_other 7.21 r_dihedral_angle_1_deg 6.648 r_scbond_it 5.419 r_scbond_other 5.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.476 r_dihedral_angle_3_deg 14.87 r_dihedral_angle_4_deg 12.605 r_lrange_it 8.979 r_lrange_other 8.779 r_scangle_it 7.212 r_scangle_other 7.21 r_dihedral_angle_1_deg 6.648 r_scbond_it 5.419 r_scbond_other 5.416 r_mcangle_it 5.161 r_mcangle_other 5.159 r_dihedral_angle_other_2_deg 5.126 r_mcbond_it 3.914 r_mcbond_other 3.912 r_angle_refined_deg 2.445 r_angle_other_deg 1.593 r_xyhbond_nbd_refined 0.418 r_chiral_restr_other 0.293 r_symmetry_xyhbond_nbd_refined 0.275 r_nbd_other 0.264 r_nbd_refined 0.242 r_symmetry_nbd_other 0.21 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.155 r_chiral_restr 0.151 r_symmetry_nbtor_other 0.093 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.026 r_gen_planes_refined 0.018 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1965 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction StructureStudio data collection PHASER phasing