1P61

Structure of human dCK complexed with 2'-Deoxycytidine and ADP, P 43 21 2 space group


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 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.001α = 90
b = 80.001β = 90
c = 93.946γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2001-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-D0.9552APS14-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
12.2300.06428.215208
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)
12.22.30.1567.5

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 DIFFRACTIONMADTHROUGHOUT2.212013671153795.790.227330.221580.27964RANDOM39.706
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]
2.172.17-4.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.942
r_scangle_it4.25
r_scbond_it2.658
r_mcangle_it2
r_angle_refined_deg1.885
r_mcbond_it1.097
r_angle_other_deg0.915
r_symmetry_hbond_refined0.395
r_symmetry_vdw_other0.3
r_symmetry_vdw_refined0.279
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.942
r_scangle_it4.25
r_scbond_it2.658
r_mcangle_it2
r_angle_refined_deg1.885
r_mcbond_it1.097
r_angle_other_deg0.915
r_symmetry_hbond_refined0.395
r_symmetry_vdw_other0.3
r_symmetry_vdw_refined0.279
r_nbd_other0.25
r_nbd_refined0.219
r_xyhbond_nbd_refined0.194
r_chiral_restr0.097
r_nbtor_other0.095
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_gen_planes_other0.007
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1869
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement