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Crystal structure of the N-formyltransferase Rv3404c from mycobacterium tuberculosis in complex with YDP-Qui4N and folinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20% PEG-8000, 100 mM HEPPS, 200 mM KCl, 5 mM TDP-Qui4N, 5 mM folinic acid
Crystal Properties Matthews coefficient Solvent content 2.59 52.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.486 α = 90 b = 73.018 β = 90 c = 173.265 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 Bruker Platinum 135 montel 2017-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.6 50 99.1 0.078 12.4 6.4 79772
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 1.6 1.7 96.8 0.351 2.5 3.2
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4pzu 1.6 50 75782 3990 99.1 0.16841 0.16673 0.20025 0.203 RANDOM 17.699
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] 0.67 -0.03 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.211 r_dihedral_angle_4_deg 16.192 r_dihedral_angle_3_deg 11.655 r_long_range_B_refined 6.567 r_long_range_B_other 6.567 r_dihedral_angle_1_deg 6.088 r_scangle_other 4.539 r_scbond_it 2.964 r_scbond_other 2.955 r_mcangle_other 2.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.211 r_dihedral_angle_4_deg 16.192 r_dihedral_angle_3_deg 11.655 r_long_range_B_refined 6.567 r_long_range_B_other 6.567 r_dihedral_angle_1_deg 6.088 r_scangle_other 4.539 r_scbond_it 2.964 r_scbond_other 2.955 r_mcangle_other 2.575 r_mcangle_it 2.574 r_angle_refined_deg 1.913 r_mcbond_it 1.761 r_mcbond_other 1.756 r_angle_other_deg 0.938 r_chiral_restr 0.112 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 3741 Nucleic Acid Atoms Solvent Atoms 666 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing