3CXQ

Crystal structure of human glucosamine 6-phosphate N-acetyltransferase 1 bound to GlcN6P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HUZPDB ENTRY 2HUZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52890.2M Na formate, 25% w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4449.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.136α = 90
b = 54.136β = 90
c = 138.638γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000Montel mirrors2008-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
12.354.34890.380.0639.26.048884
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)
2.32.460.3221.3

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 2HUZ2.320886142490.210.2090.2070.255RANDOM25.641
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]
1.61.6-3.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.35
r_dihedral_angle_3_deg15.451
r_dihedral_angle_4_deg12.718
r_dihedral_angle_1_deg5.57
r_scangle_it1.595
r_angle_refined_deg1.139
r_scbond_it0.959
r_mcangle_it0.752
r_mcbond_it0.437
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.35
r_dihedral_angle_3_deg15.451
r_dihedral_angle_4_deg12.718
r_dihedral_angle_1_deg5.57
r_scangle_it1.595
r_angle_refined_deg1.139
r_scbond_it0.959
r_mcangle_it0.752
r_mcbond_it0.437
r_nbtor_refined0.294
r_symmetry_hbond_refined0.239
r_nbd_refined0.185
r_symmetry_vdw_refined0.182
r_xyhbond_nbd_refined0.14
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1430
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms16

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
LSCALEdata scaling