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Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with adenylylimidodiphosphate, the ATP analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 283 30% MPD, 0.5M Ammonium sulfate, 0.1M HEPES pH7.5
Crystal Properties Matthews coefficient Solvent content 2.33 47.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.746 α = 90 b = 36.79 β = 123.82 c = 89.8 γ = 90
Symmetry Space Group C 1 2 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 2017-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9791 SSRF BL17U1
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 2 74.61 99.9 0.096 12.5 4.9 22161
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 2 2.05 100 0.509 3.1 4.9
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 5XOE 2 74.61 21068 1091 99.82 0.20633 0.2042 0.2129 0.24797 0.252 RANDOM 27.33
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] 0.82 0.28 -1.38 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.833 r_dihedral_angle_4_deg 18.308 r_dihedral_angle_3_deg 17.041 r_long_range_B_refined 6.963 r_long_range_B_other 6.963 r_dihedral_angle_1_deg 6.559 r_scangle_other 5.488 r_mcangle_it 3.713 r_mcangle_other 3.712 r_scbond_it 3.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.833 r_dihedral_angle_4_deg 18.308 r_dihedral_angle_3_deg 17.041 r_long_range_B_refined 6.963 r_long_range_B_other 6.963 r_dihedral_angle_1_deg 6.559 r_scangle_other 5.488 r_mcangle_it 3.713 r_mcangle_other 3.712 r_scbond_it 3.527 r_scbond_other 3.526 r_mcbond_it 2.523 r_mcbond_other 2.513 r_angle_refined_deg 2.093 r_angle_other_deg 1.119 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2412 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing