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Mycobacterium tuberculosis RmlA in complex with dTDP-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 20% poly(ethylene glycol) 3350, 200 mM KCl, 100 mM CHES
Crystal Properties Matthews coefficient Solvent content 2.34 47.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.323 α = 90 b = 111.264 β = 90 c = 290.363 γ = 90
Symmetry Space Group P 21 21 21
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 2017-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9794 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.85 50 97.7 0.103 45.8 6.5 195396
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 93.8 0.179 14.9 4.5
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 6B5K 1.85 50 185587 9779 97.74 0.17358 0.17125 0.1822 0.21758 0.2249 RANDOM 26.419
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] -0.1 1.13 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.624 r_dihedral_angle_4_deg 18.901 r_dihedral_angle_3_deg 15.147 r_dihedral_angle_1_deg 7.072 r_long_range_B_refined 5.965 r_long_range_B_other 5.965 r_scangle_other 4.499 r_mcangle_it 3.583 r_mcangle_other 3.583 r_scbond_it 3.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.624 r_dihedral_angle_4_deg 18.901 r_dihedral_angle_3_deg 15.147 r_dihedral_angle_1_deg 7.072 r_long_range_B_refined 5.965 r_long_range_B_other 5.965 r_scangle_other 4.499 r_mcangle_it 3.583 r_mcangle_other 3.583 r_scbond_it 3.066 r_scbond_other 3.066 r_mcbond_it 2.649 r_mcbond_other 2.647 r_angle_refined_deg 1.655 r_angle_other_deg 0.846 r_chiral_restr 0.197 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 17459 Nucleic Acid Atoms Solvent Atoms 1477 Heterogen Atoms 526
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing