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Crystal structure of Casein kinase I homolog 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M sodium malonate, 20 % polyethylene glycol 3350, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.78 55.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.503 α = 90 b = 97.918 β = 93.89 c = 84.737 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 CCD RAYONIX MX225HE 2016-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.8 50 98.4 27 3.7 67599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 86.6 0.575 2 3.2
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 3UYS 1.8 50 65536 1951 98.41 0.16104 0.1597 0.2085 0.2093 RANDOM 43.195
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] -2.72 -1.05 2.42 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.784 r_sphericity_bonded 28.181 r_dihedral_angle_4_deg 13.487 r_dihedral_angle_3_deg 12.914 r_dihedral_angle_1_deg 5.576 r_long_range_B_other 5.041 r_long_range_B_refined 5.037 r_scangle_other 4.768 r_mcangle_it 4.272 r_mcangle_other 4.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.784 r_sphericity_bonded 28.181 r_dihedral_angle_4_deg 13.487 r_dihedral_angle_3_deg 12.914 r_dihedral_angle_1_deg 5.576 r_long_range_B_other 5.041 r_long_range_B_refined 5.037 r_scangle_other 4.768 r_mcangle_it 4.272 r_mcangle_other 4.271 r_scbond_other 4.167 r_scbond_it 4.166 r_mcbond_it 3.551 r_mcbond_other 3.533 r_rigid_bond_restr 2.658 r_angle_refined_deg 1.226 r_angle_other_deg 0.899 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4750 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing MOLREP phasing