4WPG

Group A Streptococcus GacA is an essential dTDP-4-dehydrorhamnose reductase (RmlD)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M sodium oxamate) and 0.1 M MES/imidazole pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.2545.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.482α = 66.3
b = 45.977β = 81.21
c = 48.867γ = 95.27
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2012-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.89ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.143.894.0322.53.71081722
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1485.55.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.143.77102724544594.030.13020.12890.15494RANDOM17.021
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]
-0.720.29-0.070.59-0.51-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.638
r_dihedral_angle_4_deg23.087
r_sphericity_free11.602
r_dihedral_angle_3_deg11.415
r_rigid_bond_restr10.222
r_sphericity_bonded6.647
r_dihedral_angle_1_deg5.921
r_long_range_B_refined2.364
r_scangle_other2.274
r_long_range_B_other2.227
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.638
r_dihedral_angle_4_deg23.087
r_sphericity_free11.602
r_dihedral_angle_3_deg11.415
r_rigid_bond_restr10.222
r_sphericity_bonded6.647
r_dihedral_angle_1_deg5.921
r_long_range_B_refined2.364
r_scangle_other2.274
r_long_range_B_other2.227
r_angle_refined_deg2.073
r_scbond_it1.984
r_scbond_other1.98
r_mcangle_other1.74
r_mcangle_it1.713
r_angle_other_deg1.529
r_mcbond_it1.479
r_mcbond_other1.446
r_chiral_restr0.275
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_gen_planes_other0.004
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2268
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Cootmodel building
PHENIXphasing