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Crystal structure of variant T52P of the intracellular chorismate mutase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 0.2 M Sodium malonate, 0.1 M Bis Tris propane pH=8.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.59 α = 90 b = 59.59 β = 90 c = 46.579 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 4M 2018-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.967700 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.635 36.698 88.1 0.075 0.081 0.029 0.995 15.7 8.7 9569
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.635 1.716 33.4 0.445 9.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5MPV 1.635 36.698 9124 445 88.11 0.241 0.2402 0.248 0.2645 0.254 32.922
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] 0.207 0.207 -0.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.895 r_dihedral_angle_3_deg 17.68 r_dihedral_angle_4_deg 17.242 r_lrange_it 9.543 r_lrange_other 9.537 r_scangle_it 7.175 r_scangle_other 7.168 r_dihedral_angle_1_deg 5.556 r_scbond_it 4.478 r_scbond_other 4.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.895 r_dihedral_angle_3_deg 17.68 r_dihedral_angle_4_deg 17.242 r_lrange_it 9.543 r_lrange_other 9.537 r_scangle_it 7.175 r_scangle_other 7.168 r_dihedral_angle_1_deg 5.556 r_scbond_it 4.478 r_scbond_other 4.472 r_mcangle_it 4.274 r_mcangle_other 4.27 r_mcbond_it 3.114 r_mcbond_other 3.074 r_angle_refined_deg 1.711 r_angle_other_deg 1.401 r_symmetry_nbd_refined 0.594 r_symmetry_xyhbond_nbd_refined 0.451 r_nbd_other 0.247 r_xyhbond_nbd_refined 0.241 r_nbd_refined 0.233 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.159 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 596 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing