4LXQ

Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTdp and 5-N-Formyl-THF


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LXTpdb entry 4LXT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729511-15% PEG 8000, 200 mM NaCl, 5 mM dTDP, 5 mM N5-formyl-THF, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.160.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.861α = 90
b = 63.259β = 110.04
c = 136.212γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2012-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9794APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.430970.0460.04656.74.8148911148911
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4591.70.0770.07718.82.914019

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 4LXT1.430148911141466744596.890.159310.158270.17848RANDOM16.596
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]
-0.1-0.070.7-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.753
r_dihedral_angle_4_deg16.421
r_dihedral_angle_3_deg12.297
r_dihedral_angle_1_deg7.337
r_scangle_it5.384
r_scbond_it3.507
r_mcangle_it2.337
r_angle_refined_deg1.874
r_mcbond_it1.433
r_chiral_restr0.131
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.753
r_dihedral_angle_4_deg16.421
r_dihedral_angle_3_deg12.297
r_dihedral_angle_1_deg7.337
r_scangle_it5.384
r_scbond_it3.507
r_mcangle_it2.337
r_angle_refined_deg1.874
r_mcbond_it1.433
r_chiral_restr0.131
r_gen_planes_refined0.013
r_bond_refined_d0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4511
Nucleic Acid Atoms
Solvent Atoms1016
Heterogen Atoms221

Software

Software
Software NamePurpose
HKL-3000data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling