2JEO

Crystal structure of human uridine-cytidine kinase 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.8-1.0 M SUCCINIC ACID PH 6.7-7.3
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.971α = 90
b = 67.971β = 90
c = 236.1γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.53099.90.0925.418.6120142
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6499.90.467.217.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1RXJ2.529.451140257299.90.2050.2040.24RANDOM20.91
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]
-0.09-0.04-0.090.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.421
r_dihedral_angle_4_deg19.975
r_dihedral_angle_3_deg16.821
r_dihedral_angle_1_deg5.009
r_scangle_it2.508
r_scbond_it1.689
r_mcangle_it1.302
r_angle_refined_deg1.191
r_mcbond_it0.732
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.421
r_dihedral_angle_4_deg19.975
r_dihedral_angle_3_deg16.821
r_dihedral_angle_1_deg5.009
r_scangle_it2.508
r_scbond_it1.689
r_mcangle_it1.302
r_angle_refined_deg1.191
r_mcbond_it0.732
r_nbtor_refined0.305
r_symmetry_hbond_refined0.235
r_nbd_refined0.203
r_symmetry_vdw_refined0.14
r_xyhbond_nbd_refined0.139
r_chiral_restr0.082
r_bond_refined_d0.01
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_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1715
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing