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Human phosphoglycerate kinase in with mixture of products and substrates produced by cross-soaking a TSA crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WZB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 crystals were initially produced from 50 mM Tris (pH 7.5), 20 mM DTT, 25 mM MgCl2, 50 mM 3PG, and 10 mM ADP, supplemented with 20 mM NH4F and 1 mM deferoxamine; in 28-33% PEG 2000 MME and 0.1 M Bis/Tris pH 6.5
then cross-soaked with 35% PEG 2000 MME; 0.1 M Bis/Tris pH 6.5, 20 mM DTT, and 50 mM 3PG and 0.1mM deferoxamine
Crystal Properties Matthews coefficient Solvent content 2.21 44.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.43 α = 90 b = 92.01 β = 90 c = 108.61 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 100 PIXEL DECTRIS EIGER2 XE 9M 2012-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.933 Diamond I04-1
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 1.44 37.06 98.48 0.03 0.042 0.03 0.999 14.2 1.9 71262 15.43
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 1.44 1.49 97.8 0.353 0.499 0.353 0.737 2.4 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.44 37.06 1.34 71254 3604 98.48 0.1423 0.1411 0.1421 0.1662 0.1659 21.82
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 13.0669 f_angle_d 0.8799 f_chiral_restr 0.0681 f_plane_restr 0.0057 f_bond_d 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3116 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHENIX phasing