2PUT

The crystal structure of isomerase domain of glucosamine-6-phosphate synthase from Candida albicans


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 30% v/v 2-methyl-2,4-pentanediol, 10-fold excess of UDP-GlcNAc and Glc-6-P; crystals soaked with large excess of Fru-6-P, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.448.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.028α = 90
b = 118.188β = 91.78
c = 100.032γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.81620EMBL/DESY, HAMBURGX11

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
11.92099.70.0822712065112065123.2
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)
11.91.9398.40.56936.15965

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2POC1.919.9412011111769224191000.171650.171650.170740.21508RANDOM25.584
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_deg32.026
r_dihedral_angle_4_deg17.896
r_dihedral_angle_3_deg14.524
r_dihedral_angle_1_deg6.607
r_scangle_it4.618
r_scbond_it2.892
r_mcangle_it1.86
r_angle_refined_deg1.687
r_mcbond_it1.054
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.026
r_dihedral_angle_4_deg17.896
r_dihedral_angle_3_deg14.524
r_dihedral_angle_1_deg6.607
r_scangle_it4.618
r_scbond_it2.892
r_mcangle_it1.86
r_angle_refined_deg1.687
r_mcbond_it1.054
r_nbtor_refined0.307
r_nbd_refined0.217
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.147
r_chiral_restr0.115
r_metal_ion_refined0.11
r_symmetry_metal_ion_refined0.035
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10705
Nucleic Acid Atoms
Solvent Atoms748
Heterogen Atoms232

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling