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X-Ray structure of Human Deoxycytidine Kinase in complex with ADP and an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P60
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M sodium acetate, 25% PEG 4000, 8% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.65 53.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.238 α = 90 b = 80.238 β = 90 c = 93.95 γ = 90
Symmetry Space Group P 43 21 2
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 NOIR-1 2004-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.12 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 60.97 19463 19463
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1P60 2 60.97 19463 1056 96.13 0.22322 0.2203 0.2258 0.27795 RANDOM 48.185
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] 1.61 1.61 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.548 r_dihedral_angle_3_deg 16.678 r_dihedral_angle_4_deg 14.723 r_dihedral_angle_1_deg 5.311 r_scangle_it 2.598 r_scbond_it 1.634 r_angle_refined_deg 1.349 r_mcangle_it 1.347 r_mcbond_it 0.753 r_symmetry_hbond_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.548 r_dihedral_angle_3_deg 16.678 r_dihedral_angle_4_deg 14.723 r_dihedral_angle_1_deg 5.311 r_scangle_it 2.598 r_scbond_it 1.634 r_angle_refined_deg 1.349 r_mcangle_it 1.347 r_mcbond_it 0.753 r_symmetry_hbond_refined 0.312 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1908 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement