2FVK

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FTYPDB entry 2fty

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529320% PEG 3350, 0.1M ammonium sulfate, 1mM CaCl2, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.13α = 90
b = 71.6β = 91.4
c = 161.89γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.931ESRFID14-3

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
12.454.2399.20.097112.9803808038043.1
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)
12.42.5395.70.3292.32.611234

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2fty2.454.238036380363408599.140.180640.177840.23352RANDOM34.204
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]
-0.9-1.872.76-1.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.861
r_dihedral_angle_4_deg17.567
r_dihedral_angle_3_deg15.297
r_dihedral_angle_1_deg5.885
r_scangle_it1.508
r_angle_refined_deg1.179
r_scbond_it1.013
r_mcangle_it0.458
r_nbtor_refined0.301
r_mcbond_it0.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.861
r_dihedral_angle_4_deg17.567
r_dihedral_angle_3_deg15.297
r_dihedral_angle_1_deg5.885
r_scangle_it1.508
r_angle_refined_deg1.179
r_scbond_it1.013
r_mcangle_it0.458
r_nbtor_refined0.301
r_mcbond_it0.257
r_symmetry_vdw_refined0.238
r_nbd_refined0.189
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.137
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16594
Nucleic Acid Atoms
Solvent Atoms1043
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling