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Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium in complex with ADP, PL-linked to Lys233 via a Schiff base
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DDM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.5 293 50% PEG 4000, 10% Glycerol, 100mM Tris
Crystal Properties Matthews coefficient Solvent content 2.61 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.7 α = 90 b = 73.7 β = 90 c = 248.31 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 MARMOSAIC 225 mm CCD 2013-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 39.94 100 0.11 0.12 0.03 15.5 14.4 36036 28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 100 0.45 0.46 0.11 5.8 15.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2DDM 2.2 39.9 34098 1766 99.95 0.21175 0.21023 0.2143 0.24226 0.2345 RANDOM 33.055
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] 1.49 1.49 -2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.196 r_dihedral_angle_4_deg 15.46 r_dihedral_angle_3_deg 11.598 r_dihedral_angle_1_deg 4.649 r_long_range_B_refined 3.784 r_long_range_B_other 3.716 r_mcangle_it 1.344 r_mcangle_other 1.344 r_scangle_other 1.081 r_angle_refined_deg 0.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.196 r_dihedral_angle_4_deg 15.46 r_dihedral_angle_3_deg 11.598 r_dihedral_angle_1_deg 4.649 r_long_range_B_refined 3.784 r_long_range_B_other 3.716 r_mcangle_it 1.344 r_mcangle_other 1.344 r_scangle_other 1.081 r_angle_refined_deg 0.883 r_mcbond_it 0.733 r_mcbond_other 0.732 r_angle_other_deg 0.654 r_scbond_it 0.609 r_scbond_other 0.609 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4055 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing