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Crystal Structure of LdtMt2 (56-408) with a panipenem adduct at the active site cysteine-354
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D7H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 300 17% v/v PEG mono-methyl ester 5000 and 180 mM ammonium sulfate, Crystals were soaked in 4 mM of panipenem for 15 minutes
Crystal Properties Matthews coefficient Solvent content 2.87 57.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.06 α = 90 b = 94.06 β = 92.7 c = 75.4 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2015-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.102 51.175 91.94 30 3.6 45570
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5D7H 2.102 51.175 1.38 45570 2297 91.91 0.1638 0.1618 0.2006 0.2061
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 14.64 f_angle_d 1.134 f_chiral_restr 0.064 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5316 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 134
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing