2FVM

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the reaction product N-carbamyl-beta-alanine


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 trisodium citrate, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.141α = 90
b = 73.027β = 91.98
c = 164.105γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2005-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.843EMBL/DESY, HAMBURGBW7B

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
12.444596.10.0912.13.4773287732829.6
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)
12.442.57740.2144.837593

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2fty2.4544.3773390392297.260.184770.181990.23743RANDOM22.93
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]
-0.03-0.31.07-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.516
r_dihedral_angle_4_deg17.95
r_dihedral_angle_3_deg15.033
r_dihedral_angle_1_deg5.803
r_scangle_it1.237
r_angle_refined_deg1.177
r_scbond_it0.795
r_mcangle_it0.387
r_nbtor_refined0.3
r_mcbond_it0.231
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.516
r_dihedral_angle_4_deg17.95
r_dihedral_angle_3_deg15.033
r_dihedral_angle_1_deg5.803
r_scangle_it1.237
r_angle_refined_deg1.177
r_scbond_it0.795
r_mcangle_it0.387
r_nbtor_refined0.3
r_mcbond_it0.231
r_symmetry_vdw_refined0.221
r_nbd_refined0.187
r_symmetry_hbond_refined0.166
r_xyhbond_nbd_refined0.132
r_chiral_restr0.08
r_metal_ion_refined0.048
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16600
Nucleic Acid Atoms
Solvent Atoms795
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling