3B9X

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q8FPDB ENTRY 1Q8F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1M Tris-HCl, 0.2M NaCl, 24% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.112α = 67.9
b = 82.406β = 79.59
c = 90.163γ = 89.65
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic2007-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.310095.40.1020.09518.77.35014850148-328.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4592.60.2550.2358.96.75843

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 1Q8F2.381.924858748587156095.580.2030.2010.255RANDOM22.98
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]
1.190.540.51-0.230.02-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.082
r_dihedral_angle_4_deg17.026
r_dihedral_angle_3_deg15.107
r_dihedral_angle_1_deg6.368
r_scangle_it4.728
r_scbond_it3.759
r_mcangle_it3.389
r_mcbond_it2.516
r_angle_refined_deg1.473
r_symmetry_vdw_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.082
r_dihedral_angle_4_deg17.026
r_dihedral_angle_3_deg15.107
r_dihedral_angle_1_deg6.368
r_scangle_it4.728
r_scbond_it3.759
r_mcangle_it3.389
r_mcbond_it2.516
r_angle_refined_deg1.473
r_symmetry_vdw_refined0.303
r_nbtor_refined0.301
r_symmetry_hbond_refined0.259
r_nbd_refined0.205
r_xyhbond_nbd_refined0.163
r_metal_ion_refined0.13
r_chiral_restr0.092
r_bond_refined_d0.016
r_gen_planes_refined0.005
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 Atoms9030
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing