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S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.72 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CWB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein 6.9 mg/mL, 1 mM AMPCPP, 1 mM inhibitor, 2 mM magnesium chloride,0.186 M sodium nitrate, 18.4%w/v PEG3000, 50 mM sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.25 α = 90 b = 84.25 β = 90 c = 52.411 γ = 120
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 2015-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 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 1.72 42.57 100 0.124 20.3 20.2 22673
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 1.72 1.75 100 0.959 5 20.1
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 4CWB 1.72 42.57 21515 1131 99.98 0.18181 0.18052 0.1891 0.20717 0.2118 RANDOM 12.834
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] 0.3 0.15 0.3 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.288 r_dihedral_angle_4_deg 15.389 r_dihedral_angle_3_deg 10.639 r_dihedral_angle_1_deg 6.466 r_long_range_B_refined 5.727 r_long_range_B_other 5.52 r_scangle_other 3.755 r_angle_other_deg 3.551 r_scbond_it 2.507 r_scbond_other 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.288 r_dihedral_angle_4_deg 15.389 r_dihedral_angle_3_deg 10.639 r_dihedral_angle_1_deg 6.466 r_long_range_B_refined 5.727 r_long_range_B_other 5.52 r_scangle_other 3.755 r_angle_other_deg 3.551 r_scbond_it 2.507 r_scbond_other 2.48 r_angle_refined_deg 1.853 r_mcangle_other 1.642 r_mcangle_it 1.634 r_mcbond_it 1.111 r_mcbond_other 1.063 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_other 0.013 r_gen_planes_refined 0.008 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 1264 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building Aimless data scaling MOLREP phasing