2FTY

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NFGPDB entry 1nfg

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529320% PEG 3350, 0.1M ammonium sulfate, 0.001mM zinc chloride, 0.1M bis-tris , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.428α = 90
b = 73.32β = 91.59
c = 162.181γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.931ESRFID14-2

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
12.444.399.30.08613.53.1836298362944.9
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)
12.42.5398.70.3093.2312084

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 REPLACEMENTTHROUGHOUTPDB entry 1nfg2.443.857922679226423398.980.219960.217120.2737RANDOM35.905
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]
-0.10.412.7-2.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.512
r_dihedral_angle_4_deg17.679
r_dihedral_angle_3_deg15.726
r_dihedral_angle_1_deg5.872
r_scangle_it1.548
r_angle_refined_deg1.193
r_scbond_it0.983
r_mcangle_it0.493
r_nbtor_refined0.3
r_mcbond_it0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.512
r_dihedral_angle_4_deg17.679
r_dihedral_angle_3_deg15.726
r_dihedral_angle_1_deg5.872
r_scangle_it1.548
r_angle_refined_deg1.193
r_scbond_it0.983
r_mcangle_it0.493
r_nbtor_refined0.3
r_mcbond_it0.296
r_symmetry_hbond_refined0.246
r_symmetry_vdw_refined0.228
r_nbd_refined0.191
r_xyhbond_nbd_refined0.158
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16587
Nucleic Acid Atoms
Solvent Atoms681
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
EPMRphasing