2PUV

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 2-amino-2-deoxy-D-mannitol 6-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4148.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.121α = 90
b = 118.167β = 91.87
c = 100.137γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8162EMBL/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
11.92099.60.058224.112093412093423.2
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)
11.91.9394.70.4742.33.85743

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 REPLACEMENTTHROUGHOUT2POC1.919.9312050711808324241000.172030.172030.171210.21164RANDOM25.539
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_deg32.678
r_dihedral_angle_4_deg19.009
r_dihedral_angle_3_deg14.65
r_dihedral_angle_1_deg5.831
r_scangle_it4.533
r_scbond_it2.882
r_mcangle_it1.812
r_angle_refined_deg1.675
r_mcbond_it1.033
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.678
r_dihedral_angle_4_deg19.009
r_dihedral_angle_3_deg14.65
r_dihedral_angle_1_deg5.831
r_scangle_it4.533
r_scbond_it2.882
r_mcangle_it1.812
r_angle_refined_deg1.675
r_mcbond_it1.033
r_nbtor_refined0.307
r_nbd_refined0.218
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.148
r_symmetry_vdw_refined0.139
r_chiral_restr0.12
r_metal_ion_refined0.101
r_symmetry_metal_ion_refined0.047
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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 Atoms10658
Nucleic Acid Atoms
Solvent Atoms769
Heterogen Atoms232

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling