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Human platelet phosphofructokinase in an R-state in complex with ADP and F6P, crystal form I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WLO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 292 0.1 M KCl, 0.025 M MgCl2, 0.05 M Na Cacodylate, 15% iso-Propanol
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.652 α = 90 b = 164.524 β = 102.96 c = 133.2 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 PSI PILATUS 6M 2014-02-06 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 2.67 50 99.1 0.1 0.112 13.55 5 89992 -3 55.81
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 2.67 2.83 97.1 0.745 0.834 2.08
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 4WLO 2.67 46.03 85491 4500 99.1 0.21826 0.21634 0.2188 0.25515 0.2554 RANDOM 63.405
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] 0.29 1.16 3.68 -4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.091 r_dihedral_angle_3_deg 18.361 r_dihedral_angle_4_deg 17.062 r_long_range_B_refined 10.451 r_long_range_B_other 10.451 r_dihedral_angle_1_deg 5.728 r_scangle_other 5.647 r_mcangle_it 5.153 r_mcangle_other 5.153 r_scbond_it 3.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.091 r_dihedral_angle_3_deg 18.361 r_dihedral_angle_4_deg 17.062 r_long_range_B_refined 10.451 r_long_range_B_other 10.451 r_dihedral_angle_1_deg 5.728 r_scangle_other 5.647 r_mcangle_it 5.153 r_mcangle_other 5.153 r_scbond_it 3.449 r_scbond_other 3.446 r_mcbond_it 3.164 r_mcbond_other 3.164 r_angle_refined_deg 1.48 r_angle_other_deg 1.347 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 21936 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing PDB_EXTRACT data extraction XSCALE data scaling