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Crystal structure of CK1 delta in complex with PK-09-82
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 4.6 277.15 10% PEG 3350, 0.1M sodium sulfate, 0.1M citrate 4.6
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.438 α = 70.27 b = 85.24 β = 74.1 c = 89.678 γ = 86.86
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 2018-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
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 2.3 70.03 94 0.118 0.17 0.096 0.978 5.4 2.9 55296
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 2.3 2.42 96.8 0.413 0.602 0.337 0.832 2.1 2.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6RU8 2.3 70.03 52393 2609 93.49 0.2544 0.2519 0.2589 0.3051 0.3094 RANDOM 35.529
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] -0.3 0.27 0.33 0.73 -1.24 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.705 r_dihedral_angle_4_deg 20.291 r_dihedral_angle_3_deg 15.754 r_dihedral_angle_1_deg 7.126 r_angle_refined_deg 1.164 r_angle_other_deg 0.847 r_chiral_restr 0.059 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.705 r_dihedral_angle_4_deg 20.291 r_dihedral_angle_3_deg 15.754 r_dihedral_angle_1_deg 7.126 r_angle_refined_deg 1.164 r_angle_other_deg 0.847 r_chiral_restr 0.059 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9282 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 192
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing