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E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.40 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 8.55 293 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 calcium chloride
Crystal Properties Matthews coefficient Solvent content 1.98 37.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.88 α = 90 b = 57.89 β = 115.12 c = 38.61 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 1.4 34.96 99.8 0.111 9.3 7 28184
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 1.4 1.42 99.9 0.678 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ETK 1.4 34.96 26803 1356 99.79 0.18421 0.18231 0.1923 0.21898 0.2271 RANDOM 12.657
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] 0.16 0.26 -0.25 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_sphericity_free 25.609 r_dihedral_angle_4_deg 21.438 r_rigid_bond_restr 14.369 r_dihedral_angle_3_deg 12.069 r_sphericity_bonded 7.946 r_dihedral_angle_1_deg 6.915 r_long_range_B_refined 3.965 r_scangle_other 3.769 r_long_range_B_other 3.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_sphericity_free 25.609 r_dihedral_angle_4_deg 21.438 r_rigid_bond_restr 14.369 r_dihedral_angle_3_deg 12.069 r_sphericity_bonded 7.946 r_dihedral_angle_1_deg 6.915 r_long_range_B_refined 3.965 r_scangle_other 3.769 r_long_range_B_other 3.758 r_angle_other_deg 3.698 r_scbond_it 3.592 r_scbond_other 3.577 r_mcangle_it 2.579 r_mcangle_other 2.578 r_angle_refined_deg 2.503 r_mcbond_it 2.306 r_mcbond_other 2.157 r_chiral_restr 0.176 r_bond_refined_d 0.041 r_gen_planes_other 0.038 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 1275 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction MOLREP phasing Aimless data scaling