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Crystal structure of nucleoside diphosphate kinase B from Trypanosoma brucei bound to CDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F36 PDB ENTRY 4F36
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 TrbrA.00438.a.B1 PS01459 at 20.2 mg/mL against 40% MPD, 5% PEG8000, 0.1 M sodium cacodylate, pH 6.5, 2 mM CDP, 10 mM magnesium chloride, crystal tracking ID 234284b5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.63 α = 90 b = 121.37 β = 90 c = 112.87 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+ VariMax 2012-05-12 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 1.7 50 98.1 0.079 32.77 8.5 54412 53372 -3 21.523
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 1.74 90.2 0.438 3.24
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 4F36 1.7 41.33 53338 2628 98.09 0.1536 0.1521 0.1607 0.1821 0.1899 RANDOM 14.9271
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] -0.12 0.06 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.928 r_dihedral_angle_4_deg 24.263 r_dihedral_angle_3_deg 11.387 r_dihedral_angle_1_deg 5.715 r_angle_refined_deg 1.525 r_angle_other_deg 0.936 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.928 r_dihedral_angle_4_deg 24.263 r_dihedral_angle_3_deg 11.387 r_dihedral_angle_1_deg 5.715 r_angle_refined_deg 1.525 r_angle_other_deg 0.936 r_chiral_restr 0.09 r_bond_refined_d 0.011 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 3526 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 86
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection