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Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in ligand-free form
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 9.3 293 0.1M CHES, 0.2M NaCl, 1.4M ammonium sulfate, pH 9.3, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 39.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.359 α = 90 b = 85.359 β = 90 c = 160.822 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 210r 2010-06-22 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 2.1 50 100 0.097 11.4 12 35578 35578 27.2
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 2.1 2.21 100 0.413 8.3 9.6
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 2.1 42.68 32351 1669 95.81 0.23779 0.23574 0.2388 0.27663 0.2421 RANDOM 36.876
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.378 r_dihedral_angle_4_deg 17.311 r_dihedral_angle_3_deg 17.18 r_dihedral_angle_1_deg 5.69 r_scangle_it 1.481 r_angle_refined_deg 1.223 r_scbond_it 0.97 r_mcangle_it 0.515 r_mcbond_it 0.29 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.378 r_dihedral_angle_4_deg 17.311 r_dihedral_angle_3_deg 17.18 r_dihedral_angle_1_deg 5.69 r_scangle_it 1.481 r_angle_refined_deg 1.223 r_scbond_it 0.97 r_mcangle_it 0.515 r_mcbond_it 0.29 r_chiral_restr 0.08 r_bond_refined_d 0.009 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 4706 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling