☰ Navigation Tabs
Crystal structure of STK17B with bound dovitinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277.15 10% PEG 3350, 0.2M NaCl and 0.1M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.72 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.289 α = 90 b = 84.289 β = 90 c = 114.17 γ = 90
Symmetry Space Group P 41 2 2
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 PILATUS3 6M 2017-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
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 2.08 47.27 100 0.117 0.128 0.04 0.995 10.7 10.2 25428
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 2.08 2.14 100 0.849 0.964 0.329 0.474 2.3 8.4
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 3LM0 2.08 47.27 24201 1195 99.95 0.1872 0.1856 0.219 0.2251 RANDOM 47.402
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] 0.59 0.59 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.342 r_dihedral_angle_4_deg 21.704 r_dihedral_angle_3_deg 14.346 r_dihedral_angle_1_deg 5.865 r_angle_refined_deg 1.423 r_angle_other_deg 0.872 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.342 r_dihedral_angle_4_deg 21.704 r_dihedral_angle_3_deg 14.346 r_dihedral_angle_1_deg 5.865 r_angle_refined_deg 1.423 r_angle_other_deg 0.872 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2352 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 49
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing