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Crystal structure of a Mycobacterium tuberculosis chorismate mutase optimized for high autonomous activity by directed evolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 25% PEG MME 2000, 0.2 M trimehylamino-N-oxide, 0.1 M Tris. Microseeding.
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.587 α = 90 b = 54.587 β = 90 c = 63.217 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 MARMOSAIC 225 mm CCD 2016-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.953723 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.488 47.27 95.5 0.056 0.999 15.01 6.2 16797
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.488 1.496 82.9 2.806 0.332 0.33 2.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2W1A 1.49 47.27 15948 831 95.38 0.1911 0.18954 0.1992 0.21875 0.224 RANDOM 49.423
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] 1.34 0.67 1.34 -4.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.578 r_dihedral_angle_4_deg 16.999 r_dihedral_angle_3_deg 13.923 r_long_range_B_refined 11.125 r_long_range_B_other 11.033 r_scangle_other 8.265 r_mcangle_it 7.181 r_mcangle_other 7.176 r_dihedral_angle_1_deg 6.007 r_scbond_it 5.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.578 r_dihedral_angle_4_deg 16.999 r_dihedral_angle_3_deg 13.923 r_long_range_B_refined 11.125 r_long_range_B_other 11.033 r_scangle_other 8.265 r_mcangle_it 7.181 r_mcangle_other 7.176 r_dihedral_angle_1_deg 6.007 r_scbond_it 5.731 r_scbond_other 5.675 r_mcbond_it 4.945 r_mcbond_other 4.942 r_angle_refined_deg 1.892 r_angle_other_deg 1.086 r_chiral_restr 0.108 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 607 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing