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Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with ADP-mizoribine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.1 293 0.1M Na citrate, 13% PEG 3350, pH 5.1, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.583 α = 90 b = 164.654 β = 90 c = 182.54 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 ADSC QUANTUM 315 2010-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.55 50 99.9 0.072 25.9 7 97659 12.3
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) 1 1.55 1.58 100 0.438 5.9 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.55 31.31 92736 4856 99.89 0.16809 0.16652 0.1688 0.19826 0.1649 RANDOM 17.722
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] -0.29 -0.44 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.695 r_dihedral_angle_4_deg 17.242 r_dihedral_angle_3_deg 14.838 r_dihedral_angle_1_deg 5.964 r_scangle_it 4.747 r_scbond_it 2.976 r_mcangle_it 1.941 r_angle_refined_deg 1.901 r_mcbond_it 1.122 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.695 r_dihedral_angle_4_deg 17.242 r_dihedral_angle_3_deg 14.838 r_dihedral_angle_1_deg 5.964 r_scangle_it 4.747 r_scbond_it 2.976 r_mcangle_it 1.941 r_angle_refined_deg 1.901 r_mcbond_it 1.122 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4833 Nucleic Acid Atoms Solvent Atoms 705 Heterogen Atoms 98
Software Software Software Name Purpose ADSC data collection SHELX model building SOLVE phasing RESOLVE model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing RESOLVE phasing