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dihydrodipicolinate synthase from C. jejuni, Y110F mutation with pyruvate and Lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOUR DIFFUSION, HANGING DROP 8.5 288 17% PEG4000, 0.2 M sodium acetate, 0.1 mM TRIS, pH 8.5, VAPOUR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.14 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.983 α = 90 b = 97.61 β = 92.06 c = 131.398 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 CCD RAYONIX MX300HE 2012-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9796 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 43.45 99.9 0.147 4.5 4.17 116487 116487 43.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.784 1.4 4.24 11634
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4LY8 2.2 43.446 1.34 116434 116434 5833 99.84 0.2172 0.2172 0.2145 0.217 0.2689 0.2675 random 50.2732
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 14.01 f_angle_d 0.86 f_chiral_restr 0.057 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18178 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 206
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction MxDC data collection