2JF2

Nucleotide substrate binding by UDP-N-acetylglucosamine acyltransferase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LXAPDB ENTRY 1LXA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.510% PEG 10000, 0.1M MES, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.5652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.402α = 90
b = 95.402β = 90
c = 95.402γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.847.731000.0610.74270922
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.999.80.382.14.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1LXA1.867.4225709135899.90.1650.1630.214RANDOM22.92
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.676
r_dihedral_angle_4_deg23.588
r_dihedral_angle_3_deg14.121
r_dihedral_angle_1_deg8.555
r_scangle_it6.774
r_scbond_it5.098
r_mcangle_it3.29
r_mcbond_it2.671
r_angle_refined_deg1.301
r_symmetry_vdw_refined0.342
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.676
r_dihedral_angle_4_deg23.588
r_dihedral_angle_3_deg14.121
r_dihedral_angle_1_deg8.555
r_scangle_it6.774
r_scbond_it5.098
r_mcangle_it3.29
r_mcbond_it2.671
r_angle_refined_deg1.301
r_symmetry_vdw_refined0.342
r_nbtor_refined0.304
r_nbd_refined0.206
r_symmetry_hbond_refined0.177
r_xyhbond_nbd_refined0.162
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms1985
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing