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Crystal structure of Type III pantothenate kinase from Burkholderia thailandensis, apo structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O5F pdb entry 4O5F, pantothenate-bound structure, residues 85-150
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Rigaku Reagents, JCSG+ c5: 800mM KH2PO4, 800mm Na2HPO4, 100mM HEPES/NaOH pH 7.5; ButhA.17924.a.A1.PD0391 at 20.0mg/ml, tray 251248c5, puck iyg6-15, cryo: 25% EG in two steps, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.15 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.94 α = 90 b = 95.94 β = 90 c = 109.2 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 315r 2013-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.03320 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 99.3 0.043 0.043 24.85 7.1 56674 56269 -3 30.6
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 97.8 0.376 4.67
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 4O5F, pantothenate-bound structure, residues 85-150 1.7 50 56674 56234 2797 99.36 0.1631 0.1631 0.1619 0.1739 0.1864 0.1941 RANDOM 29.2943
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] 0.72 0.72 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.375 r_dihedral_angle_4_deg 12.256 r_dihedral_angle_3_deg 11.614 r_dihedral_angle_1_deg 5.66 r_mcangle_it 2.167 r_angle_refined_deg 1.548 r_mcbond_it 1.393 r_mcbond_other 1.376 r_angle_other_deg 1.201 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.375 r_dihedral_angle_4_deg 12.256 r_dihedral_angle_3_deg 11.614 r_dihedral_angle_1_deg 5.66 r_mcangle_it 2.167 r_angle_refined_deg 1.548 r_mcbond_it 1.393 r_mcbond_other 1.376 r_angle_other_deg 1.201 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3635 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 30
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction