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Ligand-free structure of human platelet phosphofructokinase in an R-state, crystal form I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unpublished low resolution structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 0.1 M KCl, 0.025 M MgCl2, 0.05 M Na Cacodylate, 15% iso-Propanol
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.343 α = 90 b = 178.062 β = 104.45 c = 133.117 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2013-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.89 50 99.3 0.077 0.091 13.1 3.6 79810 -3 67.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 3.06 98.1 0.573 0.676 2.11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE unpublished low resolution structure 2.89 46.97 1.36 79780 3991 99.35 0.212 0.2107 0.2104 0.2363 0.2357 Random selection 96.17
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.462 f_angle_d 1.092 f_chiral_restr 0.042 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22012 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing Coot model building PHENIX refinement PDB_EXTRACT data extraction XSCALE data reduction