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Crystal structure of Mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase in complex with substrate analog sinefungin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BV0 PDB ENTRY 3BV0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 20% PEGMME 5000, 0.1M bistris buffer, pH 7.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 41.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.627 α = 90 b = 83.43 β = 90 c = 157.988 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 120 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2.18 50 98.7 0.074 33.4 12.5 43477
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) 2.18 2.3 95.7 0.36 7 12.3
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 3BV0 2.18 35 41263 2198 98.69 0.18119 0.17855 0.1753 0.2322 0.2268 RANDOM 27.27
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] -0.9 0.96 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.061 r_dihedral_angle_3_deg 15.801 r_dihedral_angle_4_deg 14.658 r_scangle_it 6.06 r_dihedral_angle_1_deg 5.87 r_scbond_it 4.653 r_mcangle_it 3.238 r_mcbond_it 2.274 r_angle_refined_deg 1.213 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.061 r_dihedral_angle_3_deg 15.801 r_dihedral_angle_4_deg 14.658 r_scangle_it 6.06 r_dihedral_angle_1_deg 5.87 r_scbond_it 4.653 r_mcangle_it 3.238 r_mcbond_it 2.274 r_angle_refined_deg 1.213 r_nbtor_refined 0.316 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.08 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 6247 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 57
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling