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Crystal structure of Type III pantothenate kinase from Burkholderia thailandensis in complex with pantothenate and phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F9T pdb entry 2f9t, modified with CCP4 program chainsaw, search with two domains
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 Rigaku Reagents, Wizard 3/4 c8 : 40mM KH2PO4, 16% PEG 8000, 20 % glycerol; ButhA.17924.a.A1.PS01175 at 18.1mg/ml, 5mM pantothenate, 5mM ATP, 5mM MgCl2, tray 250051c8, puck jqa3-7, direct cryo, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.44 α = 90 b = 99.44 β = 90 c = 112.9 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 RAYONIX MX-225 2013-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.55 50 99.8 0.048 26.42 9.8 82475 82347 -3 26.493
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 1.55 1.59 99.9 0.575 3.82
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2f9t, modified with CCP4 program chainsaw, search with two domains 1.55 50 82475 82268 4176 99.85 0.1575 0.1575 0.1562 0.1677 0.183 0.1935 RANDOM 27.1303
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] -0.17 -0.17 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_4_deg 17.683 r_dihedral_angle_3_deg 12.895 r_dihedral_angle_1_deg 5.693 r_mcangle_it 1.626 r_angle_refined_deg 1.568 r_mcbond_it 0.968 r_mcbond_other 0.968 r_angle_other_deg 0.84 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_4_deg 17.683 r_dihedral_angle_3_deg 12.895 r_dihedral_angle_1_deg 5.693 r_mcangle_it 1.626 r_angle_refined_deg 1.568 r_mcbond_it 0.968 r_mcbond_other 0.968 r_angle_other_deg 0.84 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3682 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 88
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction