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Fragment screening of FosAKP, cryo structure in complex with fragment F2X-entry D07
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 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.125 α = 90 b = 89.785 β = 90 c = 44.899 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 1.118 54.271 84.7 0.059 0.062 0.017 1 20.9 12 90660 11.18
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 1.118 1.137 28.6 0.812 0.949 0.417 0.551 1.3 3.8
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 MIR FREE R-VALUE 1.12 54.27 1.35 90640 4445 84.7 0.135 0.134 0.1346 0.1541 0.1544 15
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 13.4775 f_angle_d 0.9928 f_chiral_restr 0.0765 f_plane_restr 0.0097 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2144 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement PHENIX phasing autoPROC data processing Coot model building XDS data reduction Aimless data scaling