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The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with NAG-NAM(tetrapeptide)
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 0.1 M HEPES pH 7 + 10% PEG 8000 + 10% Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 3.29 62.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.51 α = 90 b = 92.558 β = 90 c = 276.064 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 2017-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979080 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 2.98 48.9 100 0.047 0.998 10 10.9 31171
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 2.98 3.14 100 1.265 0.405 11.5 11.5
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 7AJ9 2.98 48.9 29567 1537 99.96 0.2123 0.2095 0.2117 0.2663 0.2598 RANDOM 114.317
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] 0.36 -1.18 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.927 r_dihedral_angle_3_deg 16.193 r_dihedral_angle_4_deg 14.702 r_dihedral_angle_1_deg 6.815 r_angle_refined_deg 1.367 r_angle_other_deg 1.181 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.927 r_dihedral_angle_3_deg 16.193 r_dihedral_angle_4_deg 14.702 r_dihedral_angle_1_deg 6.815 r_angle_refined_deg 1.367 r_angle_other_deg 1.181 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7890 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing