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Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y9R PDB 1Y9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 297 PEG4000, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.02 19.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.77 α = 90 b = 119.77 β = 90 c = 41.5 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 69 CCD MARRESEARCH MIRRORS 2004-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979870 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.33 39.2 87.5 0.147 0.08 10.52 3.192 28454 27439
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.96 2.07 86.4 0.662 0.636 1.7 2.03 3846
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB 1Y9R 2.33 39.2 28659 24920 2519 87.5 0.228 0.2074 0.2074 0.2063 0.2639 0.259 RANDOM 44.5
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] -2.45 2.29 -2.45 4.91
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.3 c_scangle_it 2.35 c_mcangle_it 1.79 c_scbond_it 1.58 c_angle_deg 1.2 c_mcbond_it 1.08 c_improper_angle_d 0.75 c_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5622 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 72
Software Software Software Name Purpose XDS data scaling XDS data reduction BEAST model building CNS refinement BEAST phasing