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Crystal structure of pyrophosphate-dependent phosphofructokinase from Promethearchaeum syntrophicum
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 0.1 M MMT pH 9.0, 20 - 30 % PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.29 46.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.975 α = 90 b = 72.365 β = 90.872 c = 137.336 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 2.2 45.815 100 0.267 0.07 0.991 22.5 14 85910
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 2.2 2.24 100 0.986 0.261 0.889 1.4 14.1
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 2.2 45.815 85894 4332 99.986 0.221 0.2195 0.2216 0.2494 0.2491 64.448
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] -3.891 2.269 3.736 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.484 r_dihedral_angle_6_deg 14.394 r_lrange_other 12.858 r_lrange_it 12.857 r_dihedral_angle_2_deg 10.119 r_scangle_it 9.241 r_scangle_other 9.241 r_mcangle_it 8.555 r_mcangle_other 8.554 r_scbond_it 6.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.484 r_dihedral_angle_6_deg 14.394 r_lrange_other 12.858 r_lrange_it 12.857 r_dihedral_angle_2_deg 10.119 r_scangle_it 9.241 r_scangle_other 9.241 r_mcangle_it 8.555 r_mcangle_other 8.554 r_scbond_it 6.154 r_scbond_other 6.154 r_mcbond_it 5.948 r_mcbond_other 5.948 r_dihedral_angle_1_deg 5.843 r_angle_refined_deg 1.437 r_angle_other_deg 0.523 r_symmetry_xyhbond_nbd_refined 0.385 r_symmetry_nbd_refined 0.242 r_nbd_refined 0.225 r_nbd_other 0.204 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_other 0.117 r_ncsr_local_group_4 0.117 r_ncsr_local_group_2 0.115 r_ncsr_local_group_3 0.114 r_ncsr_local_group_6 0.112 r_ncsr_local_group_5 0.109 r_ncsr_local_group_1 0.104 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12160 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing