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S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.95 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 9.1 281 Protein 6.9 mg/mL 1 mM AMPCPP, 1 mM inhibitor, 0.182 MgCl2, 0.1 M tris chloride, 17.2%w/v PEG8000, 50 mM sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.28 46.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.79 α = 90 b = 68.58 β = 105.94 c = 52.99 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 1.95 40.9 99.8 0.149 10 7 24055
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 1.95 2 99.8 0.758 2.9 7.1
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 1.95 40.9 22747 1228 99.51 0.19046 0.18898 0.1956 0.21815 0.2205 RANDOM 10.637
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] -0.27 -0.6 1.47 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.306 r_dihedral_angle_4_deg 14.422 r_dihedral_angle_3_deg 12.238 r_dihedral_angle_1_deg 6.599 r_long_range_B_refined 4.211 r_long_range_B_other 4.211 r_angle_other_deg 3.569 r_scangle_other 2.623 r_angle_refined_deg 1.747 r_scbond_it 1.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.306 r_dihedral_angle_4_deg 14.422 r_dihedral_angle_3_deg 12.238 r_dihedral_angle_1_deg 6.599 r_long_range_B_refined 4.211 r_long_range_B_other 4.211 r_angle_other_deg 3.569 r_scangle_other 2.623 r_angle_refined_deg 1.747 r_scbond_it 1.718 r_scbond_other 1.717 r_mcangle_other 1.351 r_mcangle_it 1.346 r_mcbond_it 0.864 r_mcbond_other 0.852 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 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 154 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building