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Structure of KIT V654A mutant with Compound 11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T46
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 8% PEG 4000
0.1 M HEPES, pH 8.2
Crystal Properties Matthews coefficient Solvent content 2.13 42.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.682 α = 90 b = 79.906 β = 90 c = 92.24 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 103 PIXEL DECTRIS EIGER X 16M 2020-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 2.1 29.08 99 0.066 0.073 0.032 0.999 12.1 4.9 20964
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 2.1 2.16 99.8 0.651 0.735 0.333 0.757 4.7
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 2.1 29.08 19898 1035 98.59 0.16967 0.16649 0.1762 0.22993 0.2382 RANDOM 42.674
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] 0.69 -0.69 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.598 r_long_range_B_refined 8.154 r_long_range_B_other 7.955 r_dihedral_angle_2_deg 7.62 r_dihedral_angle_1_deg 6.079 r_scangle_other 2.787 r_mcangle_it 2.183 r_mcangle_other 2.183 r_scbond_it 1.776 r_scbond_other 1.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.598 r_long_range_B_refined 8.154 r_long_range_B_other 7.955 r_dihedral_angle_2_deg 7.62 r_dihedral_angle_1_deg 6.079 r_scangle_other 2.787 r_mcangle_it 2.183 r_mcangle_other 2.183 r_scbond_it 1.776 r_scbond_other 1.775 r_mcbond_it 1.363 r_mcbond_other 1.363 r_angle_refined_deg 0.847 r_angle_other_deg 0.322 r_chiral_restr 0.044 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2533 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PDB_EXTRACT data extraction REFMAC phasing