1P62

Structure of human dCK complexed with gemcitabine and ADP-MG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929820%(w/v)PEG1K, 100mM magnesium acetate, 100mM TRIS, 5mM gemcitabine, 5mM ADP, 5mM MgCl2, 5mM DTT, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5351.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.2α = 90
b = 81.2β = 90
c = 94.6γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2002-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-ID

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
11.9300.05424.211.92541230.2
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)
11.91.950.5334.7

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 DIFFRACTIONMADTHROUGHOUT1.92022863254999.510.181710.178920.20713RANDOM31.92
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]
1.461.46-2.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.912
r_scangle_it4.879
r_scbond_it3.089
r_mcangle_it2.213
r_angle_refined_deg1.78
r_mcbond_it1.26
r_angle_other_deg0.954
r_symmetry_vdw_other0.32
r_nbd_other0.244
r_nbd_refined0.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.912
r_scangle_it4.879
r_scbond_it3.089
r_mcangle_it2.213
r_angle_refined_deg1.78
r_mcbond_it1.26
r_angle_other_deg0.954
r_symmetry_vdw_other0.32
r_nbd_other0.244
r_nbd_refined0.216
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.142
r_symmetry_vdw_refined0.13
r_chiral_restr0.112
r_nbtor_other0.082
r_bond_refined_d0.021
r_gen_planes_other0.013
r_gen_planes_refined0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1892
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
SOLVEphasing