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Structure of the Mycobacterium tuberculosis Type II Dehydroquinase N12S mutant (Crystal Form 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y71 PDB ENTRY 2Y71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 26% PEG 8000, 0.2 M NA-K PHOSPHATE, 0.1 M TRIS-HCL PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.9 57.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.61 α = 90 b = 125.61 β = 90 c = 125.61 γ = 90
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 PILATUS 6M PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR) 2013-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
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 2.6 72.52 100 0.09 16.1 6.9 5170 -3 30.4
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 2.6 2.74 100 0.4 5 6.8
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 (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 PDB ENTRY 2Y71 2.6 22.21 4914 238 99.75 0.14506 0.14256 0.1499 0.19809 0.1931 RANDOM 34.462
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.651 r_dihedral_angle_3_deg 14.494 r_dihedral_angle_4_deg 13.636 r_dihedral_angle_1_deg 6.465 r_scbond_it 5.144 r_mcangle_it 4.228 r_mcbond_it 2.672 r_scangle_it 2.19 r_angle_refined_deg 1.474 r_angle_other_deg 0.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.651 r_dihedral_angle_3_deg 14.494 r_dihedral_angle_4_deg 13.636 r_dihedral_angle_1_deg 6.465 r_scbond_it 5.144 r_mcangle_it 4.228 r_mcbond_it 2.672 r_scangle_it 2.19 r_angle_refined_deg 1.474 r_angle_other_deg 0.771 r_mcbond_other 0.615 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.179 r_nbd_other 0.177 r_symmetry_vdw_other 0.162 r_symmetry_hbond_refined 0.13 r_nbtor_other 0.084 r_chiral_restr 0.079 r_xyhbond_nbd_other 0.023 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_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1018 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling MOLREP phasing