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Streptococcus pyogenes GapN in complex with imidazoline-2,4-dione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PKC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 BisTris buffer pH 6.7
Li2SO4
polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.153 α = 76.94 b = 97.154 β = 77.99 c = 100.702 γ = 68.28
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 PILATUS3 S 6M 2022-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.57 46.58 82.24 0.06996 0.08173 0.04199 0.999 12.46 3.7 430858 15.41
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 1.57 1.626 0.8566 0.9949 0.5044 0.599 1.5
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 1.57 46.58 1.96 379285 19204 81.57 0.1567 0.1548 0.1549 0.1912 0.1913
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 12.596 f_angle_d 0.744 f_chiral_restr 0.048 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28432 Nucleic Acid Atoms Solvent Atoms 4556 Heterogen Atoms 224
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing