6NKJ

1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with (2R)-2-(phosphonooxy)propanoic acid.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SG1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7292Protein: 11.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (B9), 1.8M Ammonium citrate pH=7.0; Cryo: 1.8M Ammonium citrate pH=7.0, 25% Sucrose.
Crystal Properties
Matthews coefficientSolvent content
3.0760

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.713α = 90
b = 120.713β = 90
c = 70.614γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.33099.80.0490.0490.0570.02922.23.5285243-315.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.321000.5990.5990.7120.3780.7252.33.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3SG11.327.772686421385199.770.145280.144780.15494RANDOM17.4
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]
0.220.110.22-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.431
r_dihedral_angle_4_deg14.597
r_dihedral_angle_3_deg10.512
r_long_range_B_refined5.472
r_long_range_B_other4.967
r_dihedral_angle_1_deg4.474
r_scangle_other2.761
r_scbond_it1.785
r_scbond_other1.779
r_angle_refined_deg1.595
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.431
r_dihedral_angle_4_deg14.597
r_dihedral_angle_3_deg10.512
r_long_range_B_refined5.472
r_long_range_B_other4.967
r_dihedral_angle_1_deg4.474
r_scangle_other2.761
r_scbond_it1.785
r_scbond_other1.779
r_angle_refined_deg1.595
r_mcangle_it1.444
r_mcangle_other1.444
r_mcbond_it0.923
r_mcbond_other0.92
r_angle_other_deg0.413
r_chiral_restr0.075
r_gen_planes_refined0.057
r_gen_planes_other0.055
r_bond_refined_d0.007
r_bond_other_d0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6336
Nucleic Acid Atoms
Solvent Atoms1322
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing