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The structure of deoxycytidine kinase complexed with lamivudine and ADP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Reservoir containing 0.95-1.5M trisodium citrate dihydrate and 100mM HEPES, pH 7.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.64 α = 90 b = 134.24 β = 90 c = 154.86 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD mirrors 2005-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 30 95.2 0.059 12 3.1 52519 50033 -3 24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.9 74.8 0.435 2.3 2.4 6265
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1P5Z 1.8 30 44606 5027 94.48 0.19659 0.1925 0.1916 0.23328 0.2304 RANDOM 27.138
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] -0.68 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.355 r_dihedral_angle_4_deg 16.941 r_dihedral_angle_3_deg 15.777 r_dihedral_angle_1_deg 5.841 r_scangle_it 3.833 r_scbond_it 2.57 r_mcangle_it 1.817 r_angle_refined_deg 1.665 r_mcbond_it 1.125 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.355 r_dihedral_angle_4_deg 16.941 r_dihedral_angle_3_deg 15.777 r_dihedral_angle_1_deg 5.841 r_scangle_it 3.833 r_scbond_it 2.57 r_mcangle_it 1.817 r_angle_refined_deg 1.665 r_mcbond_it 1.125 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.293 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.112 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3856 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing