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S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.55 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 7.77 281 Protein 6.9 mg/mL, 1 mM AMPCPP, 1 mM inhibitor, 0.182 MgCl2, 0.1 M tris chloride, 22%w/v PEG8000, 50 mM sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.546 α = 90 b = 68.404 β = 105.94 c = 53.125 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 1.55 40.93 99.3 0.099 11.6 7.6 47134
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 1.55 1.58 98.2 0.856 2.4 7.6
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 5ETQ 1.55 40.93 44728 2384 99.16 0.15983 0.1581 0.1702 0.19195 0.2039 RANDOM 15.934
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 -0.3 1 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.477 r_dihedral_angle_4_deg 14.203 r_dihedral_angle_3_deg 11.689 r_dihedral_angle_1_deg 6.34 r_long_range_B_refined 5.317 r_long_range_B_other 5.231 r_scangle_other 4.157 r_angle_other_deg 3.576 r_scbond_it 2.833 r_scbond_other 2.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.477 r_dihedral_angle_4_deg 14.203 r_dihedral_angle_3_deg 11.689 r_dihedral_angle_1_deg 6.34 r_long_range_B_refined 5.317 r_long_range_B_other 5.231 r_scangle_other 4.157 r_angle_other_deg 3.576 r_scbond_it 2.833 r_scbond_other 2.832 r_angle_refined_deg 2.208 r_mcangle_other 2.155 r_mcangle_it 2.152 r_mcbond_it 1.481 r_mcbond_other 1.475 r_chiral_restr 0.373 r_bond_refined_d 0.023 r_gen_planes_other 0.019 r_gen_planes_refined 0.012 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2506 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building Aimless data scaling MOLREP phasing