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Structure of BFL1 in complex with a covalent inhibitor, alternative series, cmpd25
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Crystallization of adducted protein was carried out using a 2D optimization grid, (sodium citrate 0.6-1.1 M, vs PCTP buffer, 0.1 M pH 4.5-9.5). 300 nL drops (150 nL protein, 150 nL mother liquor) were incubated at 293 K in a sitting drop vapour diffusion format, dispensed using a Mosquito (SPT Labtech) and SWISSCI MRC 2-drop plates
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.634 α = 90 b = 43.382 β = 93.63 c = 62.055 γ = 90
Symmetry Space Group P 1 21 1
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 2022-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95372 Diamond I04
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 1.427 61.93 76.9 0.056 0.063 0.027 0.999 12.8 5 43147 21.57
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 1.427 1.546 18.2 0.812 0.909 0.407 0.683 1.6 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.427 61.93 43147 2219 76.8 0.1954 0.1943 0.1903 0.2143 0.2115 RANDOM 24.21
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] 0.1749 0.6613 -0.4017 0.2268
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.47 t_omega_torsion 3.16 t_angle_deg 0.98 t_bond_d 0.011 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2359 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 66
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction XDS data reduction STARANISO data scaling Aimless data scaling PHASER phasing Coot model building