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Human ARNT PAS-B complexed with KG-548 small molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EQ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M MES pH 6.5, 1.6 M magnesium sulfate, 2:1 (protein:condition)
Crystal Properties Matthews coefficient Solvent content 3.49 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.135 α = 90 b = 80.135 β = 90 c = 100.718 γ = 120
Symmetry Space Group P 31 2 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 6M 2020-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97946 NSLS-II 19-ID
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 1.97 69.4 99.76 0.049 0.05186 0.0166 0.998 22.86 10 27007 61.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.04 98.15 3.823 0.354
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.97 69.4 25028 1979 100 0.20583 0.20404 0.2115 0.22932 0.2378 RANDOM 79.074
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] -0.12 -0.06 -0.12 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.39 r_long_range_B_refined 10.56 r_long_range_B_other 10.558 r_scangle_other 8.864 r_dihedral_angle_1_deg 7.974 r_scbond_it 6.366 r_scbond_other 6.363 r_mcangle_it 6.116 r_mcangle_other 6.114 r_mcbond_other 4.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.39 r_long_range_B_refined 10.56 r_long_range_B_other 10.558 r_scangle_other 8.864 r_dihedral_angle_1_deg 7.974 r_scbond_it 6.366 r_scbond_other 6.363 r_mcangle_it 6.116 r_mcangle_other 6.114 r_mcbond_other 4.899 r_mcbond_it 4.894 r_angle_refined_deg 1.228 r_angle_other_deg 0.435 r_chiral_restr 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1765 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection autoPROC data reduction PHASER phasing PDB-REDO refinement autoPROC data scaling