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CpKRS in complex with inhibitor DDD01038762
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ELO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 protein: 30 mg/ml in 25 mM HEPES, 0.5 M NaCl, 5% glycerol, 2 mM TCEP
reservoir: 25 % PEG3350, 0.2 M Lithium sulfate, 0.1 M tris pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.595 α = 90 b = 116.129 β = 90 c = 142.036 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 PILATUS 6M 2016-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 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 1.84 116.16 100 0.088 0.053 0.999 14.4 6.3 104930
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 1.84 1.85 97 0.807 0.58 0.653 2 4.4
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 1.84 89.904 104856 5187 99.907 0.164 0.1622 0.1716 0.1933 0.1993 28.786
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] 0.001 -0.003 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.018 r_dihedral_angle_3_deg 12.814 r_dihedral_angle_2_deg 11.532 r_lrange_it 8.245 r_lrange_other 8.245 r_scangle_it 6.579 r_scangle_other 6.578 r_dihedral_angle_1_deg 6.566 r_scbond_it 4.27 r_scbond_other 4.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.018 r_dihedral_angle_3_deg 12.814 r_dihedral_angle_2_deg 11.532 r_lrange_it 8.245 r_lrange_other 8.245 r_scangle_it 6.579 r_scangle_other 6.578 r_dihedral_angle_1_deg 6.566 r_scbond_it 4.27 r_scbond_other 4.268 r_mcangle_it 3.495 r_mcangle_other 3.495 r_dihedral_angle_other_2_deg 2.836 r_mcbond_it 2.595 r_mcbond_other 2.595 r_angle_refined_deg 1.688 r_angle_other_deg 0.576 r_nbd_refined 0.21 r_nbd_other 0.205 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.165 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.154 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_1 0.059 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 8074 Nucleic Acid Atoms Solvent Atoms 739 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing Coot model building