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Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium in complex with ADP, PL-linked to Lys233 via Schiff base in protomer A and the product (PLP) in protomer B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.5 293 50% PEG 4000, 10% Glycerol, 100 mM Tris
Crystal Properties Matthews coefficient Solvent content 2.42 49.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.26 α = 90 b = 72.26 β = 90 c = 244.88 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 ROTATING ANODE RIGAKU 1.5417
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 2.45 62.23 94.3 0.13 0.14 0.03 15.7 14.9 23479 22.9
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 2.45 2.58 93 0.49 0.5 0.11 5.5 15.6
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 5ZW9 2.45 62.23 22240 1156 94.05 0.21728 0.21639 0.2211 0.23458 0.225 RANDOM 26.782
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] 0.58 0.58 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.703 r_dihedral_angle_3_deg 13.264 r_dihedral_angle_4_deg 11.835 r_dihedral_angle_1_deg 4.76 r_long_range_B_refined 3.707 r_long_range_B_other 3.707 r_mcangle_it 1.204 r_mcangle_other 1.204 r_angle_refined_deg 0.999 r_scangle_other 0.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.703 r_dihedral_angle_3_deg 13.264 r_dihedral_angle_4_deg 11.835 r_dihedral_angle_1_deg 4.76 r_long_range_B_refined 3.707 r_long_range_B_other 3.707 r_mcangle_it 1.204 r_mcangle_other 1.204 r_angle_refined_deg 0.999 r_scangle_other 0.925 r_angle_other_deg 0.803 r_mcbond_it 0.651 r_mcbond_other 0.651 r_scbond_it 0.518 r_scbond_other 0.518 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3934 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing