3CXP

Crystal structure of human glucosamine 6-phosphate N-acetyltransferase 1 mutant E156A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.92890.1M K Thiocyanate, 30% w/v PEG MME 2000, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2945.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.34α = 90
b = 51.34β = 90
c = 142.61γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBSRF BEAMLINE 3W1A1.0001BSRF3W1A

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
122099.60.07842.2213549-330.437
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)
22.1299.10.41410.8

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 2HUZ2.0119.31354667899.830.20.1990.232RANDOM21.927
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]
0.650.65-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.625
r_dihedral_angle_3_deg12.424
r_dihedral_angle_4_deg11.503
r_dihedral_angle_1_deg5.425
r_scangle_it1.456
r_angle_refined_deg0.967
r_scbond_it0.913
r_mcangle_it0.715
r_mcbond_it0.441
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.625
r_dihedral_angle_3_deg12.424
r_dihedral_angle_4_deg11.503
r_dihedral_angle_1_deg5.425
r_scangle_it1.456
r_angle_refined_deg0.967
r_scbond_it0.913
r_mcangle_it0.715
r_mcbond_it0.441
r_nbtor_refined0.295
r_nbd_refined0.173
r_symmetry_vdw_refined0.16
r_symmetry_hbond_refined0.115
r_xyhbond_nbd_refined0.104
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1416
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms1

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction