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E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.46 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 6.55 293 Protein 6.6 mg/mL, 1 mM AMPCPP, 1 mM inhibitor, 2 mM Magnesium Chloride, 27.5 %w/v PEG4000, 0.1 M sodium HEPES, 0.196 M Calcium Chloride
Crystal Properties Matthews coefficient Solvent content 1.95 36.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.763 α = 90 b = 57.631 β = 115.49 c = 38.407 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 2015-09-26 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 1.46 34.67 99.8 0.097 11.6 7.1 24472
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 1.46 1.48 99.9 0.662 2.7 6.5
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 1.46 34.67 23060 1391 99.76 0.2063 0.20441 0.2136 0.23939 0.2413 RANDOM 12.946
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] 0.48 -0.42 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.376 r_dihedral_angle_4_deg 17.167 r_dihedral_angle_3_deg 11.552 r_dihedral_angle_1_deg 6.733 r_long_range_B_refined 4.291 r_long_range_B_other 4.245 r_angle_other_deg 3.558 r_scangle_other 2.781 r_angle_refined_deg 2.206 r_mcangle_it 2.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.376 r_dihedral_angle_4_deg 17.167 r_dihedral_angle_3_deg 11.552 r_dihedral_angle_1_deg 6.733 r_long_range_B_refined 4.291 r_long_range_B_other 4.245 r_angle_other_deg 3.558 r_scangle_other 2.781 r_angle_refined_deg 2.206 r_mcangle_it 2.046 r_mcangle_other 2.045 r_scbond_other 1.891 r_scbond_it 1.862 r_mcbond_it 1.358 r_mcbond_other 1.358 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_other 0.02 r_gen_planes_refined 0.011 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 1275 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling XDS data reduction MOLREP phasing