3T90

Crystal structure of glucosamine-6-phosphate N-acetyltransferase from Arabidopsis thaliana


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VEZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529530% PEG 1000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9737.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.52α = 90
b = 47.174β = 100.74
c = 42.223γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252009-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.933BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.526.999.70.13244.83.54122421167
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.531000.26614.83.51067

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 REPLACEMENTTHROUGHOUT2VEZ1.526.882007010871000.166590.164730.20111RANDOM16.894
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.766
r_dihedral_angle_4_deg24.455
r_dihedral_angle_3_deg12.833
r_scangle_it6.532
r_dihedral_angle_1_deg5.638
r_scbond_it3.924
r_mcangle_it2.466
r_angle_refined_deg2.211
r_mcbond_it1.398
r_chiral_restr0.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.766
r_dihedral_angle_4_deg24.455
r_dihedral_angle_3_deg12.833
r_scangle_it6.532
r_dihedral_angle_1_deg5.638
r_scbond_it3.924
r_mcangle_it2.466
r_angle_refined_deg2.211
r_mcbond_it1.398
r_chiral_restr0.146
r_bond_refined_d0.026
r_gen_planes_refined0.012
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1174
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms16

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling