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Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with AMP-Mg-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B1N PDB ENTRY 3B1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 0.1M Tris, 0.2M MgCl2, 20% PEG 8000, pH 8.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.222 α = 90 b = 125.222 β = 90 c = 115.002 γ = 120
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 210r 2009-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 50 99 0.083 14.7 5.6 136213 28.1
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) 1 2 2.11 100 0.419 4.3 5.3
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3B1N 2 42.35 129118 7058 99.8 0.16916 0.16728 0.162 0.20398 0.1947 RANDOM 22.941
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] 6.31 6.31 -12.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.231 r_dihedral_angle_3_deg 18.543 r_dihedral_angle_4_deg 17.976 r_dihedral_angle_1_deg 6.053 r_scangle_it 2.167 r_scbond_it 1.417 r_angle_refined_deg 1.389 r_mcangle_it 0.902 r_mcbond_it 0.501 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.231 r_dihedral_angle_3_deg 18.543 r_dihedral_angle_4_deg 17.976 r_dihedral_angle_1_deg 6.053 r_scangle_it 2.167 r_scbond_it 1.417 r_angle_refined_deg 1.389 r_mcangle_it 0.902 r_mcbond_it 0.501 r_chiral_restr 0.088 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_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 14232 Nucleic Acid Atoms Solvent Atoms 1021 Heterogen Atoms 283
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling