1P60

Structure of human dCK complexed with 2'-Deoxycytidine and ADP, Space group C 2 2 21


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.95-1.0M citrate trisodium dihydrate, 100mM Hepes, 5mM deoxycytidine, 5mM ADP, 5mM MgCl2,5mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2444.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.714α = 90
b = 132.808β = 90
c = 157.565γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2001-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-D0.9000APS14-BM-D

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
11.96300.04523.76.93936525
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)
1.9620.2913.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.963035428393698.670.164910.160660.2035RANDOM26.099
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]
-0.050.43-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.22
r_scangle_it4.522
r_scbond_it2.893
r_mcangle_it2.104
r_angle_refined_deg1.922
r_angle_other_deg1.254
r_mcbond_it1.158
r_symmetry_hbond_refined0.401
r_symmetry_vdw_refined0.3
r_symmetry_vdw_other0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.22
r_scangle_it4.522
r_scbond_it2.893
r_mcangle_it2.104
r_angle_refined_deg1.922
r_angle_other_deg1.254
r_mcbond_it1.158
r_symmetry_hbond_refined0.401
r_symmetry_vdw_refined0.3
r_symmetry_vdw_other0.294
r_nbd_other0.245
r_nbd_refined0.216
r_xyhbond_nbd_refined0.191
r_chiral_restr0.107
r_nbtor_other0.089
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_gen_planes_other0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3819
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
AMoREphasing