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The structure of deoxycytidine kinase complexed with troxacitabine 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 2.26 45.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.85 α = 90 b = 134.46 β = 90 c = 155.34 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 2.15 30 99.7 0.099 10.9 5.1 30620 30536 -3 34
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) 2.15 2.2 100 0.511 4.4 5.2 2026
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 2.15 30 27466 3070 99.78 0.20111 0.19501 0.1928 0.25493 0.2496 RANDOM 36.53
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] 0.23 -0.7 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.473 r_dihedral_angle_4_deg 18.746 r_dihedral_angle_3_deg 17.245 r_dihedral_angle_1_deg 6.092 r_scangle_it 3.851 r_scbond_it 2.608 r_mcangle_it 1.793 r_angle_refined_deg 1.718 r_mcbond_it 1.077 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.473 r_dihedral_angle_4_deg 18.746 r_dihedral_angle_3_deg 17.245 r_dihedral_angle_1_deg 6.092 r_scangle_it 3.851 r_scbond_it 2.608 r_mcangle_it 1.793 r_angle_refined_deg 1.718 r_mcbond_it 1.077 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.291 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3850 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing