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Crystal structure of Mtb aspartate decarboxylase, 6-Chlorine pyrazinoic acid complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 MES, HEPES, PEG 3350, Ammonium Chloride
Crystal Properties Matthews coefficient Solvent content 1.86 33.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.679 α = 90 b = 143.679 β = 90 c = 59.838 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 130 PIXEL DECTRIS PILATUS3 6M 2018-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.25 21.89 99.53 0.993 8.03 5.7 65250
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 96.47 0.625 1.9
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 2C45 2.25 21.89 61782 3466 99.51 0.13543 0.13384 0.1328 0.16442 0.1603 RANDOM 51.156
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] 6.71 6.71 -13.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.615 r_dihedral_angle_4_deg 17.045 r_dihedral_angle_3_deg 13.583 r_long_range_B_refined 10.768 r_long_range_B_other 10.768 r_scangle_other 9.587 r_mcangle_it 7.908 r_mcangle_other 7.907 r_scbond_it 7.249 r_scbond_other 7.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.615 r_dihedral_angle_4_deg 17.045 r_dihedral_angle_3_deg 13.583 r_long_range_B_refined 10.768 r_long_range_B_other 10.768 r_scangle_other 9.587 r_mcangle_it 7.908 r_mcangle_other 7.907 r_scbond_it 7.249 r_scbond_other 7.249 r_dihedral_angle_1_deg 6.493 r_mcbond_it 6.361 r_mcbond_other 6.357 r_angle_refined_deg 1.606 r_angle_other_deg 1.401 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10416 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHENIX phasing