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S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.32 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ETQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 281 Protein 6.9 mg/mL 1 mM AMPCPP, 1 mM inhibitor, 0.202 M MgCl2, 0.1 M tris chloride, 19.6%w/v PEG8000, 50 mM sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.26 45.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.582 α = 90 b = 68.11 β = 106.12 c = 53.227 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 CCD ADSC QUANTUM 315r 2015-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.0329 Australian Synchrotron MX2
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 1.32 45.71 100 0.077 12.8 7.4 77438
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 1.32 1.34 100 0.832 2.2 7
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 5ETQ 1.32 45.71 73521 3888 99.99 0.12535 0.12394 0.1225 0.1518 0.1503 RANDOM 14.485
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] 0.07 -0.03 0.18 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.119 r_sphericity_free 26.358 r_rigid_bond_restr 12.948 r_dihedral_angle_3_deg 11.256 r_dihedral_angle_4_deg 10.871 r_sphericity_bonded 7.638 r_dihedral_angle_1_deg 6.149 r_angle_other_deg 3.547 r_long_range_B_refined 2.918 r_long_range_B_other 2.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.119 r_sphericity_free 26.358 r_rigid_bond_restr 12.948 r_dihedral_angle_3_deg 11.256 r_dihedral_angle_4_deg 10.871 r_sphericity_bonded 7.638 r_dihedral_angle_1_deg 6.149 r_angle_other_deg 3.547 r_long_range_B_refined 2.918 r_long_range_B_other 2.747 r_scangle_other 2.267 r_angle_refined_deg 1.938 r_scbond_it 1.837 r_scbond_other 1.837 r_mcangle_other 1.515 r_mcangle_it 1.514 r_mcbond_other 1.149 r_mcbond_it 1.148 r_chiral_restr 0.382 r_bond_refined_d 0.017 r_gen_planes_other 0.016 r_gen_planes_refined 0.011 r_bond_other_d 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 2506 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building MOLREP phasing