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Structure of the pyridoxal kinase from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I5B PDB ENTRY 2I5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 50 MM HEPES, PH 7.6, 2M AMMONIUM SULPHATE 10MG/ML PROTEIN
Crystal Properties Matthews coefficient Solvent content 2.28 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.58 α = 90 b = 102.34 β = 90.98 c = 83.54 γ = 90
Symmetry Space Group P 1 21 1
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 2013-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.45 45.69 97.1 0.05 15.93 4.5 183201 1.5
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 1.45 1.5 93 0.86 1.87 4.4
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 2I5B 1.45 45.69 173936 9265 97.11 0.1325 0.13004 0.1416 0.17811 0.1857 RANDOM 21.437
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] 0.79 -0.46 -1.06 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.433 r_sphericity_free 26.463 r_dihedral_angle_4_deg 22.757 r_sphericity_bonded 13.697 r_dihedral_angle_3_deg 11.995 r_dihedral_angle_1_deg 6.119 r_rigid_bond_restr 5.817 r_scangle_other 5.703 r_long_range_B_refined 5.583 r_scbond_it 5.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.433 r_sphericity_free 26.463 r_dihedral_angle_4_deg 22.757 r_sphericity_bonded 13.697 r_dihedral_angle_3_deg 11.995 r_dihedral_angle_1_deg 6.119 r_rigid_bond_restr 5.817 r_scangle_other 5.703 r_long_range_B_refined 5.583 r_scbond_it 5.283 r_long_range_B_other 5.28 r_scbond_other 4.983 r_mcangle_other 4.317 r_mcangle_it 4.316 r_mcbond_it 3.535 r_mcbond_other 3.533 r_angle_refined_deg 1.802 r_angle_other_deg 0.905 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8290 Nucleic Acid Atoms Solvent Atoms 992 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing