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Crystal structure of CK1 delta in complex with PK-09-129
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277.15 10% PEG 3350, 0.1M sodium sulfate, 0.1M citrate 5.0
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.123 α = 71.08 b = 84.588 β = 74.1 c = 89.281 γ = 87.22
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 2019-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
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 2.6 49.53 93.9 0.127 0.185 0.098 0.986 6.4 3.4 37749
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 2.6 2.74 95.3 0.469 0.69 0.367 0.758 2.1 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6RU8 2.6 49.53 35942 1803 93.94 0.2305 0.2284 0.2734 0.2579 RANDOM 35.131
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] -0.83 0.06 -0.44 0.67 -0.73 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.674 r_dihedral_angle_4_deg 21.081 r_dihedral_angle_3_deg 16.862 r_dihedral_angle_1_deg 7.538 r_angle_refined_deg 1.191 r_angle_other_deg 1.113 r_chiral_restr 0.05 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.674 r_dihedral_angle_4_deg 21.081 r_dihedral_angle_3_deg 16.862 r_dihedral_angle_1_deg 7.538 r_angle_refined_deg 1.191 r_angle_other_deg 1.113 r_chiral_restr 0.05 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9502 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 203
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing