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Glutamylation domain, TbtB, from thiomuracin biosynthesis bound to 5'-phosphodesmethylglutamycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2 M ammonium sulfate, 15% PEG
Crystal Properties Matthews coefficient Solvent content 2.36 47.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.503 α = 90 b = 96.098 β = 98.84 c = 107.128 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX-300 2018-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.148 96.1 99.1 0.062 0.027 0.999 17.6 6.4 48184
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.148 2.185 0.727 0.311 0.877
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 6EC7 2.148 71 45754 2430 99.07 0.21557 0.21274 0.2222 0.26638 0.2673 RANDOM 48.935
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] 4.85 -2.75 -1.77 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.978 r_dihedral_angle_4_deg 19.557 r_dihedral_angle_3_deg 16.889 r_long_range_B_refined 9.484 r_long_range_B_other 9.482 r_dihedral_angle_1_deg 8.014 r_scangle_other 6.336 r_mcangle_it 6.264 r_mcangle_other 6.264 r_scbond_it 4.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.978 r_dihedral_angle_4_deg 19.557 r_dihedral_angle_3_deg 16.889 r_long_range_B_refined 9.484 r_long_range_B_other 9.482 r_dihedral_angle_1_deg 8.014 r_scangle_other 6.336 r_mcangle_it 6.264 r_mcangle_other 6.264 r_scbond_it 4.104 r_scbond_other 4.103 r_mcbond_it 4.09 r_mcbond_other 4.086 r_angle_refined_deg 1.824 r_angle_other_deg 1.073 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 6295 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing