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Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.5 uL protein + 0.5 uL buffer (20% PEG3350, 0.2 M tri-lithium citrate, pH 7.0) + 0.2 uL 40% 2,5-hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.63 53.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.928 α = 90 b = 130.938 β = 90 c = 193.022 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 MARMOSAIC 300 mm CCD 2012-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03321 APS 23-ID-B
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 1.95 40 99.86 0.129 9.2755 7.1 235112 234904
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 1.95 2.06 99.11 0.85 6.36 33760
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 1.95 39.681 234630 11741 99.778 0.188 0.186 0.1938 0.22 0.2255 RANDOM 33.063
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] -0.596 -0.639 1.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.055 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 13.616 r_dihedral_angle_1_deg 5.809 r_mcangle_it 3.144 r_mcbond_it 2.029 r_mcbond_other 2.029 r_angle_refined_deg 1.385 r_angle_other_deg 0.788 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.055 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 13.616 r_dihedral_angle_1_deg 5.809 r_mcangle_it 3.144 r_mcbond_it 2.029 r_mcbond_other 2.029 r_angle_refined_deg 1.385 r_angle_other_deg 0.788 r_chiral_restr 0.076 r_bond_refined_d 0.01 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 1023 Heterogen Atoms 371
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction