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Crystal structure of D. melanogaster deoxyribonucleoside kinase mutant N64D in complex with dTTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OE0 PDB entry 1OE0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 MES, lithium sulphate, mPEG 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.7 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.04 α = 90 b = 119.27 β = 92.59 c = 68.388 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 4 2003-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.0 ESRF ID14-4
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 2.2 44.72 99.9 65654 1 1
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) 2.2 2.32 99.9 0.07 4.1 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 1OE0 2.2 44.72 1 65654 51654 2763 99.94 0.21329 0.21202 0.2111 0.23695 0.2309 RANDOM 36.736
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] -0.22 0.54 -2.4 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.422 r_scangle_it 4.151 r_scbond_it 2.454 r_mcangle_it 1.639 r_angle_refined_deg 1.274 r_mcbond_it 0.831 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.185 r_metal_ion_refined 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.422 r_scangle_it 4.151 r_scbond_it 2.454 r_mcangle_it 1.639 r_angle_refined_deg 1.274 r_mcbond_it 0.831 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.185 r_metal_ion_refined 0.154 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6576 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling