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Crystal Structure of the apo Staphylococcus aureus phosphofructokinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 15% PEG 4000, 0.1M MES PH 6.0, 0.15M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.23 α = 90 b = 36.949 β = 123.3 c = 87.81 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 2014-06-08 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 2.98 73.39 99.5 0.105 10.5 4.6 6551
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 3 3.05 98.6 0.474 2.4 4.5
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 3U39 2.98 73.39 6240 309 99.09 0.23646 0.23299 0.2342 0.31104 0.3072 RANDOM 37.816
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] 2.02 -1.41 -0.38 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.434 r_dihedral_angle_3_deg 19.717 r_dihedral_angle_4_deg 18.417 r_long_range_B_other 11.213 r_long_range_B_refined 11.212 r_scangle_other 10.132 r_dihedral_angle_1_deg 6.819 r_scbond_it 6.576 r_scbond_other 6.573 r_mcangle_it 5.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.434 r_dihedral_angle_3_deg 19.717 r_dihedral_angle_4_deg 18.417 r_long_range_B_other 11.213 r_long_range_B_refined 11.212 r_scangle_other 10.132 r_dihedral_angle_1_deg 6.819 r_scbond_it 6.576 r_scbond_other 6.573 r_mcangle_it 5.828 r_mcangle_other 5.826 r_mcbond_it 3.677 r_mcbond_other 3.671 r_angle_refined_deg 1.612 r_angle_other_deg 1.025 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.005 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 2413 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing