2YQH

Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the substrate-binding form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YQCPDB ENTRY 2YQC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.729330% PEG 6000, 0.1M ammonium sulfate, 5% glycerol, 0.01M N-acetylglucosamine-1-phosphate, 0.1M citrate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.448.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.431α = 90.01
b = 61.804β = 97.72
c = 90.438γ = 92.88
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDRIGAKU JUPITER 2102004-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.0000SPring-8BL45XU

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
12.350930.0711.224333416.6
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)
12.32.3886.20.126.82

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 2YQC2.338.3144027218897.70.1930.1930.238RANDOM22.9
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]
2.131.291.240.63-0.63-2.76
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d894.2
c_scangle_it3.1
c_scbond_it2.15
c_mcangle_it2.1
c_angle_deg1.4
c_mcbond_it1.35
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d894.2
c_scangle_it3.1
c_scbond_it2.15
c_mcangle_it2.1
c_angle_deg1.4
c_mcbond_it1.35
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7259
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms55

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing