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Structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EK2 PDB ENTRY 4EK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 ButhA.00438.a.A1 PS01186 at 42.64 mg/mL, 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0, cryoprotectant: 15% ethylene glycol, 1mM ADP, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.94 58.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.24 α = 90 b = 91.24 β = 90 c = 90.19 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+ 2012-09-09 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 1.95 40.427 97.9 0.062 21.37 27811 -3 23.593
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 1.95 2 95.3 0.442 2.76
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 4EK2 1.95 40.427 27787 1411 97.89 0.2092 0.2076 0.215 0.2404 0.2426 RANDOM 20.4499
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] -0.42 -0.42 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.09 r_dihedral_angle_3_deg 13.132 r_dihedral_angle_4_deg 11.255 r_dihedral_angle_1_deg 5.814 r_angle_refined_deg 1.413 r_angle_other_deg 0.784 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.09 r_dihedral_angle_3_deg 13.132 r_dihedral_angle_4_deg 11.255 r_dihedral_angle_1_deg 5.814 r_angle_refined_deg 1.413 r_angle_other_deg 0.784 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2153 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 54
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction