6OMZ

Crystal Structure of Dihydropteroate synthase from Mycobacterium smegmatis with bound 6-hydroxymethylpterin-monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EYE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5290MysmA.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 coefficientSolvent content
2.6353.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.72α = 90
b = 96.41β = 90
c = 135.07γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300Beryllium Lenses2019-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8532.90498.20.0720.0780.99919.726.9072656626.165
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)RedundancyNumber Unique Reflections (All)
11.851.984.10.50.5550.8563.035.073

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1EYE1.8532.9041.3526556209498.180.15370.15090.1861RANDOM, 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
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.696
f_angle_d0.806
f_chiral_restr0.058
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1996
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms80

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MoRDaphasing