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E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.07 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ETK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.88 293 PROTEIN 6.6 MG/ML 1 MM AMPCPP, 1 MM INHIBITOR, 2 MM MAGNESIUM CHLORIDE, 22%w/v PEG4000, 0.1 M SODIUM HEPES, 0.22 M CACL2
Crystal Properties Matthews coefficient Solvent content 1.96 37.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.77 α = 90 b = 57.75 β = 115.46 c = 38.42 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 2015-04-14 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 1.07 34.69 98.6 0.097 10.1 7.1 61436
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 1.07 1.09 96.8 0.819 2 6.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ETK 1.07 34.69 58452 2970 98.65 0.12994 0.12897 0.14996 0.1614 RANDOM 10.24
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] -0.11 -0.2 0.01 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.455 r_sphericity_free 29.392 r_dihedral_angle_4_deg 18.644 r_rigid_bond_restr 17.274 r_dihedral_angle_3_deg 9.832 r_sphericity_bonded 7.208 r_dihedral_angle_1_deg 6.879 r_angle_other_deg 3.544 r_long_range_B_refined 3.124 r_long_range_B_other 2.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.455 r_sphericity_free 29.392 r_dihedral_angle_4_deg 18.644 r_rigid_bond_restr 17.274 r_dihedral_angle_3_deg 9.832 r_sphericity_bonded 7.208 r_dihedral_angle_1_deg 6.879 r_angle_other_deg 3.544 r_long_range_B_refined 3.124 r_long_range_B_other 2.721 r_scangle_other 2.049 r_angle_refined_deg 1.968 r_scbond_it 1.557 r_scbond_other 1.557 r_mcangle_it 1.525 r_mcangle_other 1.525 r_mcbond_it 1.09 r_mcbond_other 1.09 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_other 0.018 r_gen_planes_refined 0.013 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 1272 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling MOLREP phasing XDS data reduction