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Crystal structure of pyrophosphate-dependent phosphofructokinase from Promethearchaeum syntrophicum with phosphoenolpyruvate and Mg2+
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 2.29 46.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.577 α = 90 b = 71.995 β = 90.71 c = 136.754 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 2.57 45.58 99.3 0.086 0.025 0.999 18.6 12.1 53020
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 2.57 2.65 0.627 0.18 0.944 4.3
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 2.57 45.58 53004 2628 99.307 0.23 0.2282 0.2242 0.2679 0.2627 49.004
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] -4.987 0.354 5.519 -0.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.382 r_dihedral_angle_3_deg 15.934 r_dihedral_angle_6_deg 15.927 r_lrange_it 6.926 r_lrange_other 6.926 r_scangle_it 6.206 r_scangle_other 6.206 r_mcangle_it 5.295 r_mcangle_other 5.295 r_scbond_it 4.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.382 r_dihedral_angle_3_deg 15.934 r_dihedral_angle_6_deg 15.927 r_lrange_it 6.926 r_lrange_other 6.926 r_scangle_it 6.206 r_scangle_other 6.206 r_mcangle_it 5.295 r_mcangle_other 5.295 r_scbond_it 4.787 r_scbond_other 4.787 r_dihedral_angle_1_deg 4.502 r_mcbond_it 3.778 r_mcbond_other 3.773 r_angle_refined_deg 1.519 r_dihedral_angle_other_2_deg 1.073 r_angle_other_deg 0.782 r_symmetry_nbd_other 0.233 r_nbd_refined 0.232 r_nbd_other 0.23 r_symmetry_xyhbond_nbd_refined 0.215 r_symmetry_nbd_refined 0.201 r_nbtor_refined 0.187 r_ncsr_local_group_1 0.16 r_ncsr_local_group_3 0.156 r_ncsr_local_group_2 0.149 r_ncsr_local_group_4 0.142 r_ncsr_local_group_5 0.134 r_ncsr_local_group_6 0.129 r_symmetry_xyhbond_nbd_other 0.125 r_xyhbond_nbd_refined 0.124 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11326 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing