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The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with meropenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AJ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 0.1M HEPES pH 7 + 10% PEG 8000 + 10% Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.98 58.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.877 α = 90 b = 101.224 β = 90 c = 115.285 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 100 PIXEL DECTRIS PILATUS 6M 2017-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979160 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 2.55 46.386 99.9 0.068 0.997 9.2 6.7 22790
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.66 99.9 1.038 0.516 1 6.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7AJ9 2.55 46.34 22737 1104 99.838 0.212 0.209 0.2184 0.267 0.2711 64.039
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] -5.689 0.087 5.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.661 r_dihedral_angle_4_deg 20.052 r_dihedral_angle_3_deg 16.968 r_lrange_it 9.491 r_lrange_other 9.49 r_scangle_it 7.476 r_scangle_other 7.475 r_dihedral_angle_1_deg 7.293 r_mcangle_it 6.335 r_mcangle_other 6.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.661 r_dihedral_angle_4_deg 20.052 r_dihedral_angle_3_deg 16.968 r_lrange_it 9.491 r_lrange_other 9.49 r_scangle_it 7.476 r_scangle_other 7.475 r_dihedral_angle_1_deg 7.293 r_mcangle_it 6.335 r_mcangle_other 6.335 r_scbond_it 4.704 r_scbond_other 4.703 r_mcbond_it 4.14 r_mcbond_other 4.139 r_angle_refined_deg 1.452 r_angle_other_deg 1.188 r_symmetry_xyhbond_nbd_refined 0.227 r_nbd_other 0.226 r_nbd_refined 0.216 r_symmetry_nbd_other 0.193 r_symmetry_nbd_refined 0.191 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.166 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_symmetry_xyhbond_nbd_other 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3992 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing