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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 7.0, 30 mg/ml
Reservoir: 0.2 M Li2SO4, 14-18% PEG 3350, 0.1 M tris pH 7.4-7.8
Crystal Properties Matthews coefficient Solvent content 2.52 51.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.099 α = 90 b = 118.667 β = 90.376 c = 142.837 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 PILATUS 6M 2018-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
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 2.4 47.66 96.7 0.108 0.102 0.992 8.6 3.3 91915 33.59
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 2.4 2.44 97.6 0.767 0.706 0.809 1.6 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 47.657 91888 4690 96.422 0.228 0.2257 0.2324 0.263 0.2691 34.464
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] -0.143 0.419 2.515 -2.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.752 r_dihedral_angle_3_deg 13.456 r_lrange_it 6.944 r_lrange_other 6.938 r_dihedral_angle_1_deg 6.874 r_dihedral_angle_2_deg 6.829 r_scangle_it 5.267 r_scangle_other 5.257 r_mcangle_it 4.439 r_mcangle_other 4.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.752 r_dihedral_angle_3_deg 13.456 r_lrange_it 6.944 r_lrange_other 6.938 r_dihedral_angle_1_deg 6.874 r_dihedral_angle_2_deg 6.829 r_scangle_it 5.267 r_scangle_other 5.257 r_mcangle_it 4.439 r_mcangle_other 4.439 r_scbond_it 3.357 r_scbond_other 3.343 r_mcbond_it 2.965 r_mcbond_other 2.965 r_angle_refined_deg 1.244 r_angle_other_deg 0.674 r_dihedral_angle_other_2_deg 0.262 r_nbd_other 0.241 r_symmetry_xyhbond_nbd_refined 0.204 r_symmetry_nbd_other 0.201 r_nbd_refined 0.2 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.144 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.058 r_ncsr_local_group_3 0.035 r_ncsr_local_group_4 0.034 r_ncsr_local_group_5 0.034 r_symmetry_xyhbond_nbd_other 0.033 r_ncsr_local_group_1 0.033 r_ncsr_local_group_6 0.032 r_ncsr_local_group_2 0.031 r_gen_planes_other 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16187 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing