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Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with adenylylimidodiphosphate (the ATP analog) and fructose-6-phosphate
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 15% PEG4000, 0.1M MES PH 6.0 , 0.15M(NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.36 α = 90 b = 79.83 β = 90 c = 120.39 γ = 90
Symmetry Space Group I 2 2 2
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 2014-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97915 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 1.95 66.53 99.4 0.133 9.6 5.5 26662 16.7
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 1.95 2.06 100 0.377 5.3 5.5
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 5XOE 1.95 66.53 25332 1341 99.27 0.21261 0.20997 0.2216 0.26222 0.2666 RANDOM 26.846
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] 2.62 -1.3 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.584 r_dihedral_angle_4_deg 18.143 r_dihedral_angle_3_deg 15.153 r_long_range_B_refined 5.883 r_long_range_B_other 5.882 r_dihedral_angle_1_deg 5.742 r_scangle_other 4.193 r_mcangle_it 2.842 r_mcangle_other 2.841 r_scbond_it 2.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.584 r_dihedral_angle_4_deg 18.143 r_dihedral_angle_3_deg 15.153 r_long_range_B_refined 5.883 r_long_range_B_other 5.882 r_dihedral_angle_1_deg 5.742 r_scangle_other 4.193 r_mcangle_it 2.842 r_mcangle_other 2.841 r_scbond_it 2.787 r_scbond_other 2.786 r_mcbond_it 2.145 r_mcbond_other 2.142 r_angle_refined_deg 1.861 r_angle_other_deg 1.073 r_chiral_restr 0.107 r_bond_refined_d 0.017 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 2386 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing