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Staphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophosphokinase in complex with AMPCPP and an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AD6 PDB ENTRY 4AD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 281 PROTEIN 7.5 MG/ML PLUS 1MM AMPCPP PLUS 1MM INHIBITOR, AMMONIUM SULFATE 0.275 M, PEG4000 22.1% W/V, SITTING DROP, 281 K
Crystal Properties Matthews coefficient Solvent content 2.83 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.48 α = 90 b = 82.48 β = 90 c = 52.173 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 CCD 2013-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 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 2 42.1 99.7 0.22 12.2 21.5 13792
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 2 2.11 98 1.02 3.6 19.7
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 PDB ENTRY 4AD6 2 42.17 13074 685 99.61 0.16447 0.16269 0.1696 0.19961 0.2017 RANDOM 27.368
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] 0.89 0.89 0.89 -2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.75 r_dihedral_angle_4_deg 14.001 r_dihedral_angle_3_deg 12.906 r_dihedral_angle_1_deg 6.344 r_angle_refined_deg 1.362 r_angle_other_deg 0.769 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.75 r_dihedral_angle_4_deg 14.001 r_dihedral_angle_3_deg 12.906 r_dihedral_angle_1_deg 6.344 r_angle_refined_deg 1.362 r_angle_other_deg 0.769 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1273 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing