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Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7-Keto 8-aminopelargonic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FGN PDB entry 3FGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.372 α = 90 b = 105.137 β = 90 c = 151.569 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 97.6 0.064 38 13.9 46066
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 2.26 96.3 0.39 7.33 13.5
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 3FGN 2.18 32 43644 2323 97.47 0.2164 0.21381 0.2069 0.26433 0.2577 RANDOM 36.488
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] 0.93 1.01 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.318 r_dihedral_angle_3_deg 19.368 r_dihedral_angle_4_deg 18.636 r_scangle_it 7.052 r_dihedral_angle_1_deg 6.122 r_scbond_it 5.563 r_mcangle_it 4.046 r_mcbond_it 2.811 r_angle_refined_deg 1.471 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.318 r_dihedral_angle_3_deg 19.368 r_dihedral_angle_4_deg 18.636 r_scangle_it 7.052 r_dihedral_angle_1_deg 6.122 r_scbond_it 5.563 r_mcangle_it 4.046 r_mcbond_it 2.811 r_angle_refined_deg 1.471 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.241 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.224 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 6328 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 59
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling