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Crystal Structure of PLP Bound 7,8-Diaminopelargonic Acid Synthase in Mycobacterium Tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QJ5 PDB entry 1QJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 291 PEG 8000, 0.1M Tris buffer, 0.1M MgCl2, pH 7.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.047 α = 90 b = 66.47 β = 90 c = 203.377 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.541
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 2.21 35 92.9 0.073 21.3 6.2 40606
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 2.21 2.33 78.4 0.31 3.5 3.6
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 1QJ5 2.21 35 38542 2060 92.64 0.18953 0.18698 0.1833 0.23814 0.235 RANDOM 22.445
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] -0.53 -0.17 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.877 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_3_deg 15.473 r_scangle_it 6.304 r_dihedral_angle_1_deg 5.468 r_scbond_it 4.87 r_mcangle_it 3.407 r_mcbond_it 2.321 r_angle_refined_deg 1.181 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.877 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_3_deg 15.473 r_scangle_it 6.304 r_dihedral_angle_1_deg 5.468 r_scbond_it 4.87 r_mcangle_it 3.407 r_mcbond_it 2.321 r_angle_refined_deg 1.181 r_nbtor_refined 0.314 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6180 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling PHASER phasing