2PUW

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 DROP8.527720% w/v PEG 600, 0.15M KSCN, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5164.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.864α = 90
b = 148.864β = 90
c = 102.878γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2003-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8125EMBL/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
13.1512099.80.1957.75.3195261952670
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)
13.1513.2990.791.74.4971

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 REPLACEMENTTHROUGHOUT2POC3.15119.5519427190283991000.230960.230960.229880.27948RANDOM52.835
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]
0.060.06-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.931
r_dihedral_angle_3_deg21.639
r_dihedral_angle_4_deg21.443
r_dihedral_angle_1_deg6.877
r_scangle_it1.969
r_angle_refined_deg1.514
r_scbond_it1.106
r_mcangle_it1.037
r_mcbond_it0.572
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.931
r_dihedral_angle_3_deg21.639
r_dihedral_angle_4_deg21.443
r_dihedral_angle_1_deg6.877
r_scangle_it1.969
r_angle_refined_deg1.514
r_scbond_it1.106
r_mcangle_it1.037
r_mcbond_it0.572
r_nbtor_refined0.32
r_nbd_refined0.258
r_symmetry_vdw_refined0.245
r_symmetry_hbond_refined0.194
r_xyhbond_nbd_refined0.168
r_chiral_restr0.098
r_bond_refined_d0.013
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5201
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms34

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling