1Q8F

Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MASPDB entry 1MAS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7295PEGMME 3350, methanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3247.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.808α = 112.95
b = 85.707β = 101.95
c = 90.678γ = 85.92
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Mirror2003-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.781.691.50.0469.52122468-3-316.9
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)
11.71.7963.80.22131.912529

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1MAS1.743.83121220121220124791.530.15340.153480.153310.16989RANDOM15.208
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]
0.150.51-0.28-0.320.180.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.855
r_scangle_it3.336
r_scbond_it2.003
r_angle_refined_deg1.307
r_mcangle_it1.011
r_mcbond_it0.566
r_symmetry_hbond_refined0.201
r_nbd_refined0.2
r_xyhbond_nbd_refined0.14
r_symmetry_vdw_refined0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.855
r_scangle_it3.336
r_scbond_it2.003
r_angle_refined_deg1.307
r_mcangle_it1.011
r_mcbond_it0.566
r_symmetry_hbond_refined0.201
r_nbd_refined0.2
r_xyhbond_nbd_refined0.14
r_symmetry_vdw_refined0.132
r_chiral_restr0.093
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9260
Nucleic Acid Atoms
Solvent Atoms1055
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing