☰ Navigation Tabs
Closed Human phosphoglycerate kinase complex with BPG and ADP produced by cross-soaking a TSA crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WZB starting crystal complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 Produced from MgF3 TSA crystals produced in 50 mM Tris (pH 7.5), 20 mM DTT, 25 mM MgCl2, 50 mM 3PG, and 10 mM ADP and supplemented with 20 mM NH4F and 1 mM deferoxamine. Cross-soaked with 35% PEG 2000 MME; 0.1 M Bis/Tris pH 6.5, 20 mM DTT, 25 mM MgCl2, 10mM ATP and 50 mM 3PG
Crystal Properties Matthews coefficient Solvent content 2.17 43.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.845 α = 90 b = 91.626 β = 90 c = 108.734 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 83 PIXEL DECTRIS EIGER2 XE 16M 2016-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.756 70.12 99.25 0.029 0.041 0.029 0.999 12.2 1.9 39322 25.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.82 99.3 0.385 0.544 0.385 0.687 2.2 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.756 70.067 1.36 39322 2000 99.25 0.1496 0.1481 0.1777 0.1894
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 12.315 f_angle_d 1.057 f_chiral_restr 0.057 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3116 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement xia2 data scaling xia2 data reduction PHENIX phasing