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Structure of the Mycobacterium tuberculosis Type II Dehydroquinase N12S mutant (Crystal Form 1)
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 12% GLYCEROL, 1.5 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.386 α = 90 b = 94.294 β = 97.28 c = 61.354 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 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 2.7 94.29 99 0.1 10.8 3.4 11546 -3 33.8
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 2.7 2.85 99.7 0.37 3.6 3.4
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 PDB ENTRY 2Y71 2.7 60.86 10980 549 98.87 0.20525 0.20031 0.30452 0.2829 RANDOM 36.218
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] 0.99 -0.58 -0.74 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.815 r_dihedral_angle_4_deg 20.004 r_dihedral_angle_3_deg 15.333 r_dihedral_angle_1_deg 6.722 r_scbond_it 5 r_mcangle_it 2.968 r_mcbond_it 1.699 r_scangle_it 1.339 r_angle_refined_deg 1.182 r_angle_other_deg 0.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.815 r_dihedral_angle_4_deg 20.004 r_dihedral_angle_3_deg 15.333 r_dihedral_angle_1_deg 6.722 r_scbond_it 5 r_mcangle_it 2.968 r_mcbond_it 1.699 r_scangle_it 1.339 r_angle_refined_deg 1.182 r_angle_other_deg 0.711 r_mcbond_other 0.247 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.212 r_symmetry_vdw_other 0.189 r_xyhbond_nbd_refined 0.183 r_nbd_other 0.168 r_nbtor_refined 0.166 r_symmetry_hbond_refined 0.15 r_nbtor_other 0.082 r_chiral_restr 0.058 r_xyhbond_nbd_other 0.015 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 3427 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling PHASER phasing