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Crystal Structure of Dihydropteroate synthase from Mycobacterium smegmatis with bound 6-hydroxymethylpterin-monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EYE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 290 MysmA.01019.b.B1.PW38386 was crystallized at 14 mg/mL and 14 ??C with 2.5 mM 6-Hydroxymethylpterin-monophosphate and mixed 1:1 with a solution of 0.2 M ammonium citrate dibasic pH 5.0 and 20% (w/v) PEG3350, 20% ethylene glycol cryo. Tray: 308720f3, puck: bqx9-6.
Crystal Properties Matthews coefficient Solvent content 2.63 53.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.72 α = 90 b = 96.41 β = 90 c = 135.07 γ = 90
Symmetry Space Group C 2 2 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 CCD RAYONIX MX-300 Beryllium Lenses 2019-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.85 32.904 98.2 0.072 0.078 0.999 19.72 6.907 26566 26.165
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 84.1 0.5 0.555 0.856 3.03 5.073
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1EYE 1.85 32.904 1.35 26556 2094 98.18 0.1537 0.1509 0.1511 0.1861 0.1863 RANDOM, 0
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 13.696 f_angle_d 0.806 f_chiral_restr 0.058 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1996 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 80
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing