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PR X-Ray structures in agonist conformations reveal two different mechanisms for partial agonism in 11beta-substituted steroids
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZR7 PDB ENTRY 3ZR7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 20-30% POLYETHYLENE GLYCOL 3350, 0.1 M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.662 α = 90 b = 64.374 β = 96.33 c = 70.468 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 IMAGE PLATE R-AXIS MIRRORS 2011-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.9 47.4 100 0.08 9.3 4.1 40585
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 1.9 2 99.9 0.73 1.9 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3ZR7 1.9 70.04 38443 2126 99.9 0.20788 0.20549 0.2048 0.2516 0.2563 RANDOM 35.637
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] 1.18 0.53 -0.69 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.49 r_dihedral_angle_3_deg 14.571 r_dihedral_angle_4_deg 11.527 r_dihedral_angle_1_deg 5.507 r_angle_refined_deg 1.476 r_angle_other_deg 0.946 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.49 r_dihedral_angle_3_deg 14.571 r_dihedral_angle_4_deg 11.527 r_dihedral_angle_1_deg 5.507 r_angle_refined_deg 1.476 r_angle_other_deg 0.946 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4043 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction SCALA data scaling REFMAC phasing