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Structure of the pyridoxal kinase from Staphylococcus aureus in complex with AMP-PCP
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, 2M NH4SO4
Crystal Properties Matthews coefficient Solvent content 2.19 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.21 α = 90 b = 100.51 β = 90 c = 167.06 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 1.45 48.76 99.5 0.06 20.38 8.8 185724 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 96.3 1.17 1.79 8.5
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 1.45 48.76 175767 9325 99.7 0.12442 0.12197 0.1353 0.17056 0.1773 RANDOM 21.882
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] 0.39 -0.34 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.839 r_sphericity_free 28.535 r_dihedral_angle_4_deg 25.282 r_sphericity_bonded 13.583 r_dihedral_angle_3_deg 11.732 r_dihedral_angle_1_deg 6.171 r_long_range_B_refined 4.764 r_scangle_other 4.587 r_long_range_B_other 4.417 r_scbond_it 4.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.839 r_sphericity_free 28.535 r_dihedral_angle_4_deg 25.282 r_sphericity_bonded 13.583 r_dihedral_angle_3_deg 11.732 r_dihedral_angle_1_deg 6.171 r_long_range_B_refined 4.764 r_scangle_other 4.587 r_long_range_B_other 4.417 r_scbond_it 4.105 r_scbond_other 3.879 r_rigid_bond_restr 3.458 r_mcangle_it 3.271 r_mcangle_other 3.27 r_mcbond_other 2.862 r_mcbond_it 2.861 r_angle_refined_deg 1.723 r_angle_other_deg 0.831 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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 8263 Nucleic Acid Atoms Solvent Atoms 978 Heterogen Atoms 209
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling