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Crystal structure of nucleoside diphosphate kinase family protein from Babesia bovis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VU5 trimer generate from 2VU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 CSHT condition A4, 2.0 M ammonium sulfate, 0.1 M Tris pH 8.5; 0.4:0.4 uL drops; 31.2 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% glycerol, 2 mM DTT; crystal tracking ID 204382a4; non-cleavable expression tag, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.78 67.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.894 α = 90 b = 125.894 β = 90 c = 101.512 γ = 90
Symmetry Space Group P 43 21 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 ADSC QUANTUM 315 2009-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976484 ALS 5.0.3
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 2.5 50 99.5 0.149 14.3 9.2 28787
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 2.5 2.59 97.2 0.677 2.4 7.6 2742
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 trimer generate from 2VU5 2.5 47.08 28727 1464 99.27 0.179 0.176 0.187 0.221 0.2248 RANDOM 28.414
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] -2.3 -2.3 4.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.58 r_dihedral_angle_4_deg 22.979 r_dihedral_angle_3_deg 15.537 r_dihedral_angle_1_deg 5.978 r_scangle_it 3.301 r_scbond_it 2.093 r_angle_refined_deg 1.466 r_mcangle_it 1.253 r_mcbond_it 0.65 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.58 r_dihedral_angle_4_deg 22.979 r_dihedral_angle_3_deg 15.537 r_dihedral_angle_1_deg 5.978 r_scangle_it 3.301 r_scbond_it 2.093 r_angle_refined_deg 1.466 r_mcangle_it 1.253 r_mcbond_it 0.65 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3478 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 65
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling