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Crystal Structure of H. influenzae TrmD in complex with Compound 14
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 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.607 α = 90 b = 94.607 β = 90 c = 177.954 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 1.9 47.348 99.1 0.116 0.128 0.052 0.999 17.8 10.9 24197
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 1.9 1.94 1.33 1.463 0.601 0.726 10.8
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 1.9 47.348 24191 2453 98.783 0.176 0.1742 0.1745 0.1933 0.1935 27.299
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 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.348 r_dihedral_angle_3_deg 15.109 r_dihedral_angle_4_deg 12.305 r_lrange_it 7.877 r_lrange_other 7.876 r_dihedral_angle_1_deg 6.496 r_scangle_it 5.881 r_scangle_other 5.879 r_scbond_it 4.192 r_scbond_other 4.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.348 r_dihedral_angle_3_deg 15.109 r_dihedral_angle_4_deg 12.305 r_lrange_it 7.877 r_lrange_other 7.876 r_dihedral_angle_1_deg 6.496 r_scangle_it 5.881 r_scangle_other 5.879 r_scbond_it 4.192 r_scbond_other 4.182 r_mcangle_it 4.169 r_mcangle_other 4.167 r_mcbond_it 2.983 r_mcbond_other 2.976 r_angle_refined_deg 1.821 r_angle_other_deg 1.489 r_xyhbond_nbd_refined 0.288 r_symmetry_xyhbond_nbd_refined 0.238 r_nbd_other 0.236 r_nbd_refined 0.216 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.124 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.05 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 286 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction StructureStudio data collection PHASER phasing