☰ Navigation Tabs
Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex with thymidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OT3 PDB entry 1OT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 6.5 288 MES, lithium sulphate, mPEG 2000, pH 6.5, Counter diffusion, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.712 α = 90 b = 70.34 β = 90.69 c = 224.528 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 Mirrors 2003-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 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 3.1 41.17 99.9 39975 1 1
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) 3.1 3.27 99.9 0.38 3.4 3.7 39562
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1OT3 3.1 41.17 1 37947 2005 99.96 0.2696 0.26958 0.26858 0.2366 0.2884 0.2647 RANDOM 37.441
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] -0.9 2.48 2.32 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.314 r_scangle_it 2.254 r_scbond_it 1.247 r_mcangle_it 1.212 r_angle_refined_deg 1.134 r_mcbond_it 0.635 r_symmetry_hbond_refined 0.458 r_symmetry_vdw_refined 0.313 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.314 r_scangle_it 2.254 r_scbond_it 1.247 r_mcangle_it 1.212 r_angle_refined_deg 1.134 r_mcbond_it 0.635 r_symmetry_hbond_refined 0.458 r_symmetry_vdw_refined 0.313 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12536 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing