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The structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to deoxyadenosine monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DUT PDB ENTRY 4DUT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 ButhA.00438.a.A1 PS01186 at 42.64 mg/mL in 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0, 10 mM dAMP, cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.92 57.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.68 α = 90 b = 90.68 β = 90 c = 90.43 γ = 90
Symmetry Space Group P 41 2 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 RIGAKU SATURN 944 2012-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 40.553 97.2 0.066 30.21 25415 -3 19.831
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 2.05 84.4 0.219 7.95
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 4DUT 2 40.553 25383 1295 97.22 0.1916 0.1897 0.2032 0.2282 0.2365 RANDOM 16.6122
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] -0.24 -0.24 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.722 r_dihedral_angle_4_deg 18.641 r_dihedral_angle_3_deg 14.022 r_dihedral_angle_1_deg 5.729 r_scangle_it 3.149 r_scbond_it 1.885 r_angle_refined_deg 1.332 r_mcangle_it 1.103 r_angle_other_deg 0.923 r_mcbond_it 0.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.722 r_dihedral_angle_4_deg 18.641 r_dihedral_angle_3_deg 14.022 r_dihedral_angle_1_deg 5.729 r_scangle_it 3.149 r_scbond_it 1.885 r_angle_refined_deg 1.332 r_mcangle_it 1.103 r_angle_other_deg 0.923 r_mcbond_it 0.615 r_mcbond_other 0.159 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2162 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 36
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction