3DC8

Crystal structure of dihydropyrimidinase from Sinorhizobium meliloti


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YNY1YNY, 1KCX, 1K1D
experimental modelPDB 1KCX1YNY, 1KCX, 1K1D
experimental modelPDB 1K1D1YNY, 1KCX, 1K1D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1COUNTER-DIFFUSION4.62934.0M sodium formate, 0.1M sodium acetate, pH 4.6, COUNTER-DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6165.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.887α = 90
b = 126.281β = 90
c = 196.104γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000Montel mirrors2006-08-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
11.8539.8998.40.0662133.4712959314
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)
11.851.989.10.3113.111.838930

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 REPLACEMENTTHROUGHOUT1YNY, 1KCX, 1K1D1.8529.6129519652498.460.1490.1480.176RANDOM5.383
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]
0.010.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.226
r_dihedral_angle_4_deg17.585
r_dihedral_angle_3_deg11.217
r_dihedral_angle_1_deg10.5
r_scangle_it2.835
r_scbond_it2.021
r_angle_refined_deg1.644
r_mcangle_it1.168
r_mcbond_it0.918
r_angle_other_deg0.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.226
r_dihedral_angle_4_deg17.585
r_dihedral_angle_3_deg11.217
r_dihedral_angle_1_deg10.5
r_scangle_it2.835
r_scbond_it2.021
r_angle_refined_deg1.644
r_mcangle_it1.168
r_mcbond_it0.918
r_angle_other_deg0.332
r_nbtor_refined0.299
r_nbd_refined0.202
r_xyhbond_nbd_refined0.198
r_symmetry_vdw_refined0.192
r_symmetry_hbond_refined0.187
r_chiral_restr0.146
r_nbd_other0.135
r_metal_ion_refined0.056
r_bond_refined_d0.028
r_gen_planes_refined0.009
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7313
Nucleic Acid Atoms
Solvent Atoms1338
Heterogen Atoms36

Software

Software
Software NamePurpose
SAINTdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction