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Pantothenamide-bound Pantothenate Kinase from Klebsiella pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GI7 pdb entry 4GI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 289 0.5 uL protein + 0.5 uL buffer (2M sodium formate, 0.1M Tris HCl), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.84 56.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.765 α = 90 b = 180.366 β = 90 c = 181.488 γ = 90
Symmetry Space Group F 2 2 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 MARMOSAIC 300 mm CCD 2013-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 1.9 40 99.9 0.121 19.5 8.3 68657 -3
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 1.9 1.97 100 0.453 8.1
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 (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 4GI7 1.9 39.63 68701 68629 3467 99.9 0.157 0.154 0.1555 0.214 0.2169 RANDOM 34.32
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] -2.71 1.58 1.13
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.714 r_dihedral_angle_2_deg 34.893 r_sphericity_bonded 31.767 r_dihedral_angle_4_deg 18.09 r_dihedral_angle_3_deg 13.615 r_scbond_it 6.651 r_dihedral_angle_1_deg 5.509 r_mcangle_it 5.365 r_mcbond_it 4.314 r_rigid_bond_restr 2.754
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.714 r_dihedral_angle_2_deg 34.893 r_sphericity_bonded 31.767 r_dihedral_angle_4_deg 18.09 r_dihedral_angle_3_deg 13.615 r_scbond_it 6.651 r_dihedral_angle_1_deg 5.509 r_mcangle_it 5.365 r_mcbond_it 4.314 r_rigid_bond_restr 2.754 r_angle_refined_deg 1.286 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4901 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 108
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction