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Structure of the pyridoxal kinase from Staphylococcus aureus in complex with AMP-PCP and pyridoxal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C5J PDB ENTRY 4C5J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 50MM HEPES PH7.6, 2M NH4SO4
Crystal Properties Matthews coefficient Solvent content 2.21 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.19 α = 90 b = 100.66 β = 90 c = 168.21 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 PIXEL DECTRIS PILATUS 2013-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 1.75 48.26 99.8 0.15 12.6 8.8 107272 1
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 1.75 1.81 98 1.5 1 7.8
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 PDB ENTRY 4C5J 1.75 48.26 101932 5340 99.71 0.2067 0.20427 0.2109 0.25333 0.2578 RANDOM 26.636
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] 1.67 -1.2 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.96 r_dihedral_angle_4_deg 21.804 r_dihedral_angle_3_deg 14.456 r_dihedral_angle_1_deg 6.724 r_scbond_it 2.122 r_angle_refined_deg 1.938 r_mcangle_it 1.788 r_mcbond_it 1.241 r_mcbond_other 1.241 r_angle_other_deg 0.907
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.96 r_dihedral_angle_4_deg 21.804 r_dihedral_angle_3_deg 14.456 r_dihedral_angle_1_deg 6.724 r_scbond_it 2.122 r_angle_refined_deg 1.938 r_mcangle_it 1.788 r_mcbond_it 1.241 r_mcbond_other 1.241 r_angle_other_deg 0.907 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8109 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 207
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing