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Crystal structure of mineralocorticoid receptor ligand binding domain in complex with esaxerenone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MWP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 2.0-2.5 M sodium nitrate, 0.1 M Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.98 58.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.888 α = 90 b = 160.888 β = 90 c = 160.888 γ = 90
Symmetry Space Group P 21 3
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 2018-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3 19.96 99.8 0.397 0.417 0.998 5.42 10.303 27958 93.301
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.19 99.7 6.61 7.001 0.101 0.34 9.258
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 5mwp 3 19.96 26335 1441 99.39 0.2705 0.2685 0.2704 0.307 0.3079 RANDOM 116.551
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.621 r_dihedral_angle_3_deg 20.48 r_dihedral_angle_4_deg 12.311 r_dihedral_angle_1_deg 7.538 r_angle_refined_deg 1.61 r_angle_other_deg 1.173 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.621 r_dihedral_angle_3_deg 20.48 r_dihedral_angle_4_deg 12.311 r_dihedral_angle_1_deg 7.538 r_angle_refined_deg 1.61 r_angle_other_deg 1.173 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6084 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing