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Human RIOK2 bound to inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG3350, 10% ethylene glycol, 0.1 M bis-tris-propane pH 6.5 and 0.2 M sodium/potassium tartrat
Crystal Properties Matthews coefficient Solvent content 2.62 53.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.01 α = 90 b = 92.86 β = 99.1 c = 237.65 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 2M 2016-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9201 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.35 92.86 99.7 0.11 6.6 3.1 164333
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 2.35 2.39 98.3 0.59 1.8 2.8
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 4GYI 2.35 78.34 156092 8217 99.66 0.21595 0.21494 0.217 0.23543 0.237 RANDOM 53.696
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] 0.75 -0.26 -0.64 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.625 r_dihedral_angle_4_deg 23.505 r_dihedral_angle_3_deg 17.398 r_dihedral_angle_1_deg 6.299 r_long_range_B_refined 4.416 r_long_range_B_other 4.416 r_scangle_other 2.063 r_mcangle_it 1.928 r_mcangle_other 1.928 r_angle_refined_deg 1.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.625 r_dihedral_angle_4_deg 23.505 r_dihedral_angle_3_deg 17.398 r_dihedral_angle_1_deg 6.299 r_long_range_B_refined 4.416 r_long_range_B_other 4.416 r_scangle_other 2.063 r_mcangle_it 1.928 r_mcangle_other 1.928 r_angle_refined_deg 1.415 r_scbond_it 1.269 r_scbond_other 1.268 r_angle_other_deg 1.252 r_mcbond_it 1.093 r_mcbond_other 1.093 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22681 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 292
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing