4LXT

Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTdp-Qui3N and 5-N-Formyl-THF


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LXQPDB ENTRY 4LXQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1729511-15% PEG 8000, 200 mM NaCl, 5 mM N-5formyl-THF, 5 mM TDP-Qui3N, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.1160.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.775α = 90
b = 65.148β = 110.51
c = 134.718γ = 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-BMAPS19-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
11.43092.90.0450.04548.33.8143095
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)
11.41.4584.90.080.0815.52.4

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 4LXQ1.430143095135924717192.90.1790.1770.206RANDOM18.45
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]
0.14-0.170.61-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.475
r_dihedral_angle_3_deg12.993
r_dihedral_angle_4_deg11.719
r_dihedral_angle_1_deg7.545
r_scangle_it5.598
r_scbond_it3.742
r_mcangle_it2.513
r_angle_refined_deg2.071
r_mcbond_it1.672
r_chiral_restr0.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.475
r_dihedral_angle_3_deg12.993
r_dihedral_angle_4_deg11.719
r_dihedral_angle_1_deg7.545
r_scangle_it5.598
r_scbond_it3.742
r_mcangle_it2.513
r_angle_refined_deg2.071
r_mcbond_it1.672
r_chiral_restr0.142
r_bond_refined_d0.015
r_gen_planes_refined0.009
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 Atoms946
Heterogen Atoms216

Software

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