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E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.09 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q0N
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, 0.16 M CaCl2
Crystal Properties Matthews coefficient Solvent content 1.96 37.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.79 α = 90 b = 57.69 β = 115.57 c = 38.45 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 2015-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9707 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 1.09 34.68 97.7 0.073 14 7.2 57389
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 1.09 1.11 95 0.563 3.1 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 1Q0N 1.09 34.68 54545 2830 97.7 0.11672 0.11571 0.1152 0.1364 0.1351 RANDOM 10.46
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] -0.04 -0.09 -0.27 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.17 r_sphericity_free 27.331 r_dihedral_angle_4_deg 17.576 r_rigid_bond_restr 16.009 r_dihedral_angle_3_deg 9.744 r_sphericity_bonded 7.288 r_dihedral_angle_1_deg 6.656 r_angle_other_deg 3.54 r_long_range_B_refined 3.091 r_long_range_B_other 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.17 r_sphericity_free 27.331 r_dihedral_angle_4_deg 17.576 r_rigid_bond_restr 16.009 r_dihedral_angle_3_deg 9.744 r_sphericity_bonded 7.288 r_dihedral_angle_1_deg 6.656 r_angle_other_deg 3.54 r_long_range_B_refined 3.091 r_long_range_B_other 2.67 r_scangle_other 2.194 r_angle_refined_deg 1.983 r_scbond_it 1.885 r_scbond_other 1.775 r_mcangle_it 1.595 r_mcangle_other 1.594 r_mcbond_it 1.173 r_mcbond_other 1.101 r_chiral_restr 0.381 r_bond_refined_d 0.028 r_gen_planes_other 0.017 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1275 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling XDS data reduction MOLREP phasing