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CpKRS complexed with lysine and an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other internal model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein buffer: 25 mM HEPES, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP, pH 7, 30 mg/ml
Reservoir: 0.2 M Li2SO4, 14-18% PEG3350, 0.1 M tris pH 7.4-7.8
Crystal Properties Matthews coefficient Solvent content 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.987 α = 90 b = 121.761 β = 90 c = 143.092 γ = 90
Symmetry Space Group P 2 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 100 PIXEL DECTRIS EIGER2 XE 16M 2020-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97627 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 56.08 100 0.223 0.09 0.997 8.7 13.8 86869 27.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04 100 2.516 1.002 0.494 1.2 14.1
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 56.08 86793 4333 99.976 0.184 0.1822 0.2218 0.2071 33.068
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] -1.827 2.749 -0.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.504 r_dihedral_angle_3_deg 12.578 r_dihedral_angle_2_deg 8.052 r_dihedral_angle_1_deg 6.922 r_lrange_it 6.34 r_lrange_other 6.3 r_scangle_it 5.301 r_scangle_other 5.301 r_scbond_it 3.514 r_scbond_other 3.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.504 r_dihedral_angle_3_deg 12.578 r_dihedral_angle_2_deg 8.052 r_dihedral_angle_1_deg 6.922 r_lrange_it 6.34 r_lrange_other 6.3 r_scangle_it 5.301 r_scangle_other 5.301 r_scbond_it 3.514 r_scbond_other 3.514 r_mcangle_it 3.453 r_mcangle_other 3.452 r_mcbond_it 2.55 r_mcbond_other 2.549 r_angle_refined_deg 1.458 r_angle_other_deg 0.517 r_nbd_other 0.212 r_nbd_refined 0.208 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.163 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.073 r_ncsr_local_group_1 0.062 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_symmetry_xyhbond_nbd_other 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8098 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing