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Crystal Structure of D-alanine--D-alanine ligase from Klebsiella pneumoniae subsp. pneumoniae in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I12 pdb entry 3i12 as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 Anatrace/Calibre MCSG1 screen, condition B11: 200mM magnesium chloride, 100mM TrisBase / HCl pH 8.5, 20% (w/V) PEG 8000: KlpnC.00137.a.B1.PW38983 at 17mg/ml + 3mM Magensium chloride + 3mM AMP: tray: 322140 B11: cryo: 20% EG, puck: ody5-7
Crystal Properties Matthews coefficient Solvent content 2.25 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.35 α = 90 b = 115.42 β = 90 c = 68.48 γ = 90
Symmetry Space Group P 21 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 100 CCD RAYONIX MX-300 Beryllium Lenses 2022-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.85 50 100 0.081 0.088 0.998 16.16 6.136 65184 27.571
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 100 0.646 0.706 0.815 2.74 6.133
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE pdb entry 3i12 as per Morda 1.85 39.13 1.34 65179 1967 99.98 0.1628 0.1617 0.1621 0.1992 0.1994 0 24.92
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.3041 f_angle_d 0.8868 f_chiral_restr 0.0618 f_bond_d 0.0079 f_plane_restr 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5119 Nucleic Acid Atoms Solvent Atoms 755 Heterogen Atoms 84
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing Coot model building