4LY3

Crystal structure of WlaRD, a sugar 3N-formyl transferase in the presence of dTPD-Qui3N, dTDP-Qui3NFo, and THF


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LXQpdb entry 4LXQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729511-15% PEG 8000, 200 mM NaCl, 5 mM TDP, 5 mM N-5-formyl-THF, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.1260.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.003α = 90
b = 65.552β = 109.83
c = 134.501γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135mirrors2013-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.95092.80.050.0515.93.65844358443

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 4LXQ1.9505844355503294091.90.179990.177580.22617RANDOM18.94
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]
0.32-0.060.82-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.692
r_dihedral_angle_3_deg13.626
r_dihedral_angle_4_deg13.25
r_dihedral_angle_1_deg7.464
r_angle_refined_deg1.99
r_angle_other_deg0.881
r_chiral_restr0.116
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.692
r_dihedral_angle_3_deg13.626
r_dihedral_angle_4_deg13.25
r_dihedral_angle_1_deg7.464
r_angle_refined_deg1.99
r_angle_other_deg0.881
r_chiral_restr0.116
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms4472
Nucleic Acid Atoms
Solvent Atoms609
Heterogen Atoms162

Software

Software
Software NamePurpose
APEXdata collection
PHASERphasing
REFMACrefinement
APEXdata reduction