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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 15% PEG4000, 0.1M MES PH 6.0 , 0.15M(NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.56 51.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.56 α = 90 b = 80.2 β = 90 c = 121.3 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 2013-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9793 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 1.6 66.9 100 0.107 11.6 6.2 47521 12.6
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 1.6 1.69 100 0.417 4.3 5.3
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 1.6 66.9 45110 2404 99.93 0.15514 0.15389 0.1678 0.17881 0.1894 RANDOM 15.544
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] 0.56 -0.23 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.488 r_dihedral_angle_4_deg 14.811 r_dihedral_angle_3_deg 12.535 r_long_range_B_refined 6.053 r_long_range_B_other 6.053 r_dihedral_angle_1_deg 5.028 r_scangle_other 4.496 r_scbond_it 3.07 r_scbond_other 3.07 r_mcangle_other 2.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.488 r_dihedral_angle_4_deg 14.811 r_dihedral_angle_3_deg 12.535 r_long_range_B_refined 6.053 r_long_range_B_other 6.053 r_dihedral_angle_1_deg 5.028 r_scangle_other 4.496 r_scbond_it 3.07 r_scbond_other 3.07 r_mcangle_other 2.341 r_mcangle_it 2.336 r_angle_refined_deg 2.217 r_mcbond_it 1.653 r_mcbond_other 1.64 r_angle_other_deg 1.149 r_chiral_restr 0.141 r_bond_refined_d 0.026 r_gen_planes_refined 0.011 r_bond_other_d 0.004 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 2446 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing