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Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with ADP
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 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.086 α = 90 b = 36.807 β = 124.01 c = 89.862 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 2015-06-23 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 1.9 50 99.6 0.074 20.8 3.8 25669
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 1.9 1.93 0.378
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 1.9 49.36 24166 1253 98.17 0.19119 0.1892 0.2102 0.22923 0.2403 RANDOM 25.661
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] 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.187 r_dihedral_angle_3_deg 16.279 r_dihedral_angle_4_deg 12.971 r_long_range_B_refined 6.751 r_long_range_B_other 6.75 r_dihedral_angle_1_deg 6.227 r_scangle_other 4.934 r_mcangle_it 3.404 r_scbond_it 3.404 r_mcangle_other 3.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.187 r_dihedral_angle_3_deg 16.279 r_dihedral_angle_4_deg 12.971 r_long_range_B_refined 6.751 r_long_range_B_other 6.75 r_dihedral_angle_1_deg 6.227 r_scangle_other 4.934 r_mcangle_it 3.404 r_scbond_it 3.404 r_mcangle_other 3.403 r_scbond_other 3.402 r_mcbond_it 2.504 r_mcbond_other 2.49 r_angle_refined_deg 2.058 r_angle_other_deg 1.155 r_chiral_restr 0.135 r_bond_refined_d 0.019 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 2423 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MLPHARE phasing