☰ Navigation Tabs
Crystal structure of the pyrophosphate-dependent phosphofructokinase from Promethearchaeum syntrophicum with fructose 6-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 291 1 M MMT pH 9.0, 20 - 30 % PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.23 44.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.21 α = 90 b = 71.866 β = 91.079 c = 136.53 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 PIXEL DECTRIS EIGER2 S 16M 2022-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95366 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.5 45.5 100 0.148 0.053 0.996 9 7.6 51164
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.68 1.587 0.561 0.719 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.6 45.5 51113 2601 99.894 0.25 0.24172 0.2462 0.27963 0.29 49.531
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] -4.134 2.023 2.836 1.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.53 r_dihedral_angle_3_deg 15.789 r_dihedral_angle_2_deg 12.891 r_lrange_it 6.902 r_lrange_other 6.902 r_scangle_it 6.179 r_scangle_other 6.178 r_mcangle_it 5.566 r_mcangle_other 5.566 r_dihedral_angle_1_deg 5.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.53 r_dihedral_angle_3_deg 15.789 r_dihedral_angle_2_deg 12.891 r_lrange_it 6.902 r_lrange_other 6.902 r_scangle_it 6.179 r_scangle_other 6.178 r_mcangle_it 5.566 r_mcangle_other 5.566 r_dihedral_angle_1_deg 5.343 r_scbond_it 4.834 r_scbond_other 4.828 r_mcbond_it 4.029 r_mcbond_other 4.027 r_angle_refined_deg 1.582 r_angle_other_deg 0.836 r_symmetry_nbd_other 0.237 r_nbd_other 0.231 r_nbd_refined 0.225 r_nbtor_refined 0.189 r_symmetry_nbd_refined 0.167 r_ncsr_local_group_3 0.167 r_ncsr_local_group_5 0.166 r_ncsr_local_group_2 0.165 r_ncsr_local_group_4 0.161 r_ncsr_local_group_6 0.156 r_ncsr_local_group_1 0.155 r_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10789 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing