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Fragment screening of FosAKP, cryo structure in complex with fragment F2X-entry F08
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 The protein was crystallized by mixing 0.45 uL of 12 mg/mL protein solution in 10 mM Hepes, pH 7.5, 50 mM NaCl, with 0.45 uL 16% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5 and 0.1 uL crystal microseeds in 26% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5. After at least 4 days of crystal growth, 40 nL of 100 mM compound, solubilized in 100% DMSO, was added using an acoustic droplet dispensing system.
Crystal Properties Matthews coefficient Solvent content 2.11 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.124 α = 90 b = 89.717 β = 90 c = 44.96 γ = 90
Symmetry Space Group P 21 21 2
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 X 16M KB mirrors 2023-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 1.147 54.26 89.1 0.068 0.071 0.02 1 17.3 11.9 88492 12.08
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 1.147 1.166 46.6 1.039 1.163 0.501 0.629 1.1 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 1.15 54.26 1.34 88418 4321 89.07 0.1439 0.1429 0.1423 0.1631 0.1625 16.35
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 13.9817 f_angle_d 0.9711 f_chiral_restr 0.0744 f_plane_restr 0.0101 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2144 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement PHENIX phasing autoPROC data processing ARP model building XDS data reduction Aimless data scaling