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Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with N-pentylpantothenamide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.5 uL protein + 0.5 uL buffer (20% PEG3350, 0.2 M tri-lithium citrate) + 0.2 uL (+/-)-1,3-butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.837 α = 90 b = 130.825 β = 90 c = 192.15 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315 2012-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931 APS 19-ID
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 40 99.95 0.148 13.6649 7.08 187512 187511
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 2.21 99.91 0.9 6.68 27124
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.1 39.645 187327 9425 99.879 0.187 0.1852 0.1936 0.2261 0.2325 RANDOM 27.292
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] -0.826 -0.723 1.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.278 r_dihedral_angle_4_deg 19.263 r_dihedral_angle_3_deg 14.618 r_dihedral_angle_1_deg 5.913 r_mcangle_it 2.798 r_mcbond_it 1.724 r_mcbond_other 1.723 r_angle_refined_deg 1.414 r_angle_other_deg 0.772 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.278 r_dihedral_angle_4_deg 19.263 r_dihedral_angle_3_deg 14.618 r_dihedral_angle_1_deg 5.913 r_mcangle_it 2.798 r_mcbond_it 1.724 r_mcbond_other 1.723 r_angle_refined_deg 1.414 r_angle_other_deg 0.772 r_chiral_restr 0.078 r_bond_refined_d 0.013 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 19893 Nucleic Acid Atoms Solvent Atoms 987 Heterogen Atoms 396
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction