3QEO

S74E-R104M-D133A dCK variant in complex with L-deoxythymidine and UDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P5ZPDB ENTRY 1P5Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52989 mg/ml protein was mixed with 0.9-1.5M trisodium citrate di-hydrate and 100 mM Tris, pH 7.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1943.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.76α = 90
b = 68.76β = 90
c = 120.597γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.89768.6899.70.0674423144080

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 1P5Z1.89768.684423144080423898.430.199510.194690.24396RANDOM34.571
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]
-4.18-4.188.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.814
r_dihedral_angle_4_deg22.414
r_dihedral_angle_3_deg18.465
r_dihedral_angle_1_deg6.141
r_scangle_it2.705
r_scbond_it1.951
r_angle_refined_deg1.538
r_mcangle_it1.268
r_mcbond_it0.732
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.814
r_dihedral_angle_4_deg22.414
r_dihedral_angle_3_deg18.465
r_dihedral_angle_1_deg6.141
r_scangle_it2.705
r_scbond_it1.951
r_angle_refined_deg1.538
r_mcangle_it1.268
r_mcbond_it0.732
r_chiral_restr0.116
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms3879
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms84

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling