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Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WYQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1M Tris-HCl at pH 8.6-8.8, 20%(v/v) MPD, 20%(w/v) PEG1000, 5%(w/v) PEG200
Crystal Properties Matthews coefficient Solvent content 2.63 53.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.02 α = 90 b = 86.02 β = 90 c = 149.191 γ = 120
Symmetry Space Group P 32 2 1
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 ADSC QUANTUM 210r 2016-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.75 74.5 100 0.143 14 10.8 17233
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.88 100 1.202
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5WYQ 2.75 52.77 16300 893 99.97 0.18371 0.18012 0.1866 0.24877 0.2579 RANDOM 59.651
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] 0.46 0.23 0.46 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.832 r_dihedral_angle_3_deg 21.13 r_dihedral_angle_4_deg 19.825 r_long_range_B_refined 11.424 r_long_range_B_other 11.41 r_scangle_other 6.972 r_mcangle_it 6.347 r_mcangle_other 6.345 r_dihedral_angle_1_deg 5.655 r_scbond_it 4.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.832 r_dihedral_angle_3_deg 21.13 r_dihedral_angle_4_deg 19.825 r_long_range_B_refined 11.424 r_long_range_B_other 11.41 r_scangle_other 6.972 r_mcangle_it 6.347 r_mcangle_other 6.345 r_dihedral_angle_1_deg 5.655 r_scbond_it 4.427 r_scbond_other 4.426 r_mcbond_it 4.143 r_mcbond_other 4.143 r_angle_refined_deg 1.047 r_angle_other_deg 0.831 r_chiral_restr 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3820 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing