☰ Navigation Tabs
E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.05 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 9.1 281 PROTEIN 6.6 MG/ML 1 MM AMPCPP, 1 MM INHIBITOR, 2 MM MAGNESIUM CHLORIDE, 20%w/v PEG4000, 0.1 M TRIS CHLORIDE, 0.172 M CALCIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 1.97 37.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.95 α = 90 b = 57.77 β = 116.11 c = 38.64 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 1.05 34.7 99.8 0.087 13.4 7.1 66451
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 1.05 1.06 99.2 0.298 5.1 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 1Q0N 1.05 34.7 63260 3162 99.72 0.10791 0.10706 0.1071 0.12504 0.1243 RANDOM 6.66
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] -0.07 0.05 0.06 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.606 r_sphericity_free 20.21 r_dihedral_angle_4_deg 16.169 r_rigid_bond_restr 12.398 r_dihedral_angle_3_deg 10.271 r_dihedral_angle_1_deg 6.346 r_sphericity_bonded 4.797 r_angle_other_deg 3.529 r_long_range_B_refined 2.407 r_long_range_B_other 2.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.606 r_sphericity_free 20.21 r_dihedral_angle_4_deg 16.169 r_rigid_bond_restr 12.398 r_dihedral_angle_3_deg 10.271 r_dihedral_angle_1_deg 6.346 r_sphericity_bonded 4.797 r_angle_other_deg 3.529 r_long_range_B_refined 2.407 r_long_range_B_other 2.406 r_angle_refined_deg 2.099 r_scangle_other 1.196 r_scbond_it 0.931 r_scbond_other 0.931 r_mcangle_it 0.829 r_mcangle_other 0.829 r_mcbond_it 0.625 r_mcbond_other 0.625 r_chiral_restr 0.116 r_gen_planes_other 0.022 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 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 1280 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing XDS data reduction Coot model building