4LY0

Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTDP-Glc and 10-N-Formyl-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 N5-formyl-THF, 5 mM TDP, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.1260.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.641α = 90
b = 65.286β = 111.73
c = 135.805γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135mirrors2013-05-01MSINGLE 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
11.65092.80.0460.04615.63.39621296212
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)
11.9279.10.3050.3052.21.413596

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4LXQ1.645.729621291401481192.790.1730.1730.171160.20785RANDOM17.121
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]
0.26-0.280.77-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.108
r_dihedral_angle_4_deg15.613
r_dihedral_angle_3_deg13.517
r_dihedral_angle_1_deg7.532
r_angle_refined_deg2.24
r_angle_other_deg0.958
r_chiral_restr0.136
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.108
r_dihedral_angle_4_deg15.613
r_dihedral_angle_3_deg13.517
r_dihedral_angle_1_deg7.532
r_angle_refined_deg2.24
r_angle_other_deg0.958
r_chiral_restr0.136
r_bond_refined_d0.012
r_gen_planes_refined0.011
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 Atoms4498
Nucleic Acid Atoms
Solvent Atoms797
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement