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Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site
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 MICROBATCH 7.4 288.15 0.3 M Magnesium acetate, 10 % PEG8000,
0.1 M Sodium acetate (pH 7.4)
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.88 α = 90 b = 201.44 β = 108.45 c = 113.66 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 S 6M 2017-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.1 38.583 99.6 0.9 6.79 15 204501 25.94
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 2.1 2.175 99.87 0.686
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4LY8 2.1 38.583 1.34 204468 10224 99.69 0.208 0.2056 0.2066 0.2526 0.2525 27.9909
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 14.184 f_angle_d 0.613 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27298 Nucleic Acid Atoms Solvent Atoms 1572 Heterogen Atoms 466
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data reduction AMPLE phasing