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Crystal structure of human dCK R104M/D133A in complex with L-dT and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5Z PDB entry 1P5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 1 microliter of protein-nucleoside-nucleotide mix and 1 microliter reservoir solution containing 0.9-1.5 M Trisodium citrate dihydrate and 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.28 46.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.78 α = 90 b = 79.78 β = 90 c = 93.7 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 MARMOSAIC 225 mm CCD 2008-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 30 99.3 0.089 14.42 13710 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.45 98.2 0.298 6.93
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 PDB entry 1P5Z 2.31 30 11826 1310 95.16 0.21041 0.2049 0.2222 0.26108 RANDOM 45.265
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] 1.31 1.31 -2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.044 r_dihedral_angle_3_deg 18.256 r_dihedral_angle_4_deg 15.173 r_dihedral_angle_1_deg 5.261 r_scangle_it 3.055 r_scbond_it 1.983 r_mcangle_it 1.475 r_angle_refined_deg 1.402 r_mcbond_it 0.85 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.044 r_dihedral_angle_3_deg 18.256 r_dihedral_angle_4_deg 15.173 r_dihedral_angle_1_deg 5.261 r_scangle_it 3.055 r_scbond_it 1.983 r_mcangle_it 1.475 r_angle_refined_deg 1.402 r_mcbond_it 0.85 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.218 r_xyhbond_nbd_refined 0.217 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.164 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1838 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 44
Software Software Software Name Purpose XDS data scaling MOLREP phasing REFMAC refinement XDS data reduction