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Crystal structure of Mtb aspartate decarboxylase, 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 2.16 43.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.282 α = 90 b = 162.282 β = 90 c = 62.826 γ = 90
Symmetry Space Group P 41 21 2
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 2018-08-09 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 2.7 21.92 99.7 0.999 16.48 15.7 23578
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 2.7 2.796 99.87 0.774 2.31
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 2.7 21.76 22440 1140 99.71 0.20159 0.19934 0.2022 0.24666 0.2527 RANDOM 56.54
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] -0.71 -0.71 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.979 r_dihedral_angle_4_deg 18.916 r_dihedral_angle_3_deg 14.601 r_long_range_B_refined 9.155 r_long_range_B_other 9.155 r_scangle_other 7.469 r_dihedral_angle_1_deg 6.953 r_mcangle_it 6.456 r_mcangle_other 6.455 r_scbond_it 5.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.979 r_dihedral_angle_4_deg 18.916 r_dihedral_angle_3_deg 14.601 r_long_range_B_refined 9.155 r_long_range_B_other 9.155 r_scangle_other 7.469 r_dihedral_angle_1_deg 6.953 r_mcangle_it 6.456 r_mcangle_other 6.455 r_scbond_it 5.006 r_scbond_other 5.006 r_mcbond_it 4.395 r_mcbond_other 4.393 r_angle_refined_deg 1.437 r_angle_other_deg 1.351 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 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 5262 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHENIX phasing