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Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with inosine
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 4 293 0.1M Na acetate, 0.2M Ca acetate, 26% PEG 400, pH 4.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.11 α = 66.33 b = 85.897 β = 68.47 c = 86.872 γ = 67.81
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 270 2009-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 1.7 50 97.2 0.056 19.1 3.9 208756 14.8
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 1.7 1.73 94 0.376 2.8 3.6
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 1.7 47.78 198251 10501 100 0.17733 0.17578 0.1757 0.20667 0.2074 RANDOM 24.609
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] -0.36 0.96 0.16 -0.57 0.3 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.248 r_dihedral_angle_4_deg 16.092 r_dihedral_angle_3_deg 15.69 r_dihedral_angle_1_deg 6.087 r_scangle_it 4.496 r_scbond_it 2.912 r_angle_refined_deg 1.84 r_mcangle_it 1.8 r_mcbond_it 1.07 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.248 r_dihedral_angle_4_deg 16.092 r_dihedral_angle_3_deg 15.69 r_dihedral_angle_1_deg 6.087 r_scangle_it 4.496 r_scbond_it 2.912 r_angle_refined_deg 1.84 r_mcangle_it 1.8 r_mcbond_it 1.07 r_chiral_restr 0.133 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 13886 Nucleic Acid Atoms Solvent Atoms 1049 Heterogen Atoms 314
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling