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Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, UDP-bound form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 EBS internal tracking number 234285A5: JCSG A5, protein: 20.2 mg/mL TrbrA.00438.a.B1 PS01459 in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, crystallant: 20% PEG3350, 200 mM magnesium formate, 2 mM UDP, 10 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.83 α = 90 b = 121.51 β = 90 c = 113.17 γ = 90
Symmetry Space Group C 2 2 21
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+ 2012-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.541780
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 41.744 98.1 0.077 23.16 28728 -3 22.959
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 2.15 91.9 0.257 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 41.744 28728 1444 98 0.16 0.158 0.195 0.1672 RANDOM 16.846
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] 0.15 0.12 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.264 r_dihedral_angle_4_deg 26.271 r_dihedral_angle_3_deg 11.972 r_dihedral_angle_1_deg 5.808 r_angle_refined_deg 1.46 r_angle_other_deg 1.146 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.264 r_dihedral_angle_4_deg 26.271 r_dihedral_angle_3_deg 11.972 r_dihedral_angle_1_deg 5.808 r_angle_refined_deg 1.46 r_angle_other_deg 1.146 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3499 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 78
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction