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Human estrogen receptor alpha ligand-binding domain in complex with estradiol and the E2#23 FN3 monobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZKY PDB entries 1ZKY, 1FNF experimental model PDB 1FNF PDB entries 1ZKY, 1FNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 2.5M NaCl, 0.1M Imidazole, pH 8.0, 0.2M Zn(OAc)2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.91 57.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.219 α = 90 b = 119.219 β = 90 c = 132.999 γ = 120
Symmetry Space Group P 61 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 CCD ADSC QUANTUM 315 Bent Conical Si-Mirror (Rh-coated) 2006-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.97900 APS 14-BM-C
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 2.95 50 99.6 0.12 23.19 14.3 12253
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 2.95 3.06 0.685 3 10.6 1191
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 PDB entries 1ZKY, 1FNF 2.95 48.11 11540 575 98.69 0.19429 0.19146 0.25091 0.2633 RANDOM 67.996
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] 1.82 0.91 1.82 -2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.251 r_scangle_it 23.356 r_dihedral_angle_3_deg 22.802 r_dihedral_angle_4_deg 18.092 r_scbond_it 17.695 r_mcangle_it 10.435 r_mcbond_it 7.032 r_dihedral_angle_1_deg 5.651 r_angle_refined_deg 1.334 r_nbtor_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.251 r_scangle_it 23.356 r_dihedral_angle_3_deg 22.802 r_dihedral_angle_4_deg 18.092 r_scbond_it 17.695 r_mcangle_it 10.435 r_mcbond_it 7.032 r_dihedral_angle_1_deg 5.651 r_angle_refined_deg 1.334 r_nbtor_refined 0.338 r_symmetry_vdw_refined 0.322 r_nbd_refined 0.272 r_symmetry_hbond_refined 0.257 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2559 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling XFIT data reduction