4LRU

Crystal structure of glyoxalase III (Orf 19.251) from Candida albicans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RW7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.1277100 mM sodium acetate pH 4.1, 120 mM ammonium acetate, 27% PEG4000 and 3% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4249.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.23α = 90
b = 92.23β = 90
c = 59.367γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2011-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
11.6411000.0551.112.13439021
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)
11.61.6310012.212.2

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1RW71.6413421632486173099.60.1590.1580.185RANDOM25.58
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]
0.440.44-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.986
r_dihedral_angle_4_deg15.712
r_dihedral_angle_3_deg13.214
r_dihedral_angle_1_deg9.034
r_long_range_B_refined6.347
r_long_range_B_other6.346
r_scangle_other3.377
r_scbond_other2.363
r_scbond_it2.361
r_mcangle_other2.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.986
r_dihedral_angle_4_deg15.712
r_dihedral_angle_3_deg13.214
r_dihedral_angle_1_deg9.034
r_long_range_B_refined6.347
r_long_range_B_other6.346
r_scangle_other3.377
r_scbond_other2.363
r_scbond_it2.361
r_mcangle_other2.008
r_mcangle_it2.004
r_mcbond_it1.503
r_mcbond_other1.478
r_angle_refined_deg1.081
r_angle_other_deg0.63
r_chiral_restr0.077
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_gen_planes_other0.001
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1843
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms8

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling