4AG9

C. elegans glucosamine-6-phosphate N-acetyltransferase (GNA1): ternary complex with coenzyme A and GlcNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AG7PDB ENTRY 4AG7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15 MM ACCOA, GLCN-6-P, GLCNAC AND 0.1 M TRIS-HYDROCHLORIDE PH 8.5, 0.2 M SODIUM ACETATE TRIHYDRATE AND 30% (V/V) PEG 3350 AND 11 MM BACL2
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.872α = 90
b = 53.353β = 90
c = 135.096γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.752098.10.0528.13.6346332
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)
11.751.8189.50.263.53.1

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 4AG71.7614.993387871597.090.191240.190420.23216RANDOM31.121
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]
0.02-0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.288
r_dihedral_angle_4_deg17.297
r_dihedral_angle_3_deg14.289
r_dihedral_angle_1_deg6.777
r_angle_refined_deg2.289
r_chiral_restr0.141
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.288
r_dihedral_angle_4_deg17.297
r_dihedral_angle_3_deg14.289
r_dihedral_angle_1_deg6.777
r_angle_refined_deg2.289
r_chiral_restr0.141
r_bond_refined_d0.019
r_gen_planes_refined0.011
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_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 Atoms2580
Nucleic Acid Atoms
Solvent Atoms411
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing