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Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed to Burned Meat Compound PhIP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ERD PDB ENTRY 3ERD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 298 0.2M Magnesium chloride hexahydrate, 0.1M Tris 8.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.09 41.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.965 α = 90 b = 83.703 β = 108.7 c = 58.427 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 CCD MARMOSAIC 325 mm CCD FLAT MIRROR (VERTICAL FOCUSING) 2007-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 2.3 12 88.8 0.12 0.12 16.7 3.3 20199 46.85
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 2.3 2.38 86.9 0.241 0.241 3.73 3
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 (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 ENTRY 3ERD 2.3 11.96 20138 20138 1040 88.5 0.274 0.273 0.2729 0.296 0.2964 RANDOM 26.26
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] -0.26 -0.34 -0.45 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.002 r_dihedral_angle_4_deg 23.685 r_dihedral_angle_3_deg 18.729 r_scangle_it 15.056 r_scbond_it 14.837 r_mcangle_it 11.031 r_mcbond_it 10.175 r_dihedral_angle_1_deg 6.294 r_angle_other_deg 2.739 r_angle_refined_deg 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.002 r_dihedral_angle_4_deg 23.685 r_dihedral_angle_3_deg 18.729 r_scangle_it 15.056 r_scbond_it 14.837 r_mcangle_it 11.031 r_mcbond_it 10.175 r_dihedral_angle_1_deg 6.294 r_angle_other_deg 2.739 r_angle_refined_deg 1.54 r_mcbond_other 1.367 r_symmetry_hbond_refined 1.098 r_symmetry_vdw_other 0.401 r_symmetry_vdw_refined 0.268 r_nbd_other 0.256 r_nbd_refined 0.24 r_nbtor_refined 0.195 r_xyhbond_nbd_refined 0.149 r_nbtor_other 0.1 r_chiral_restr 0.093 r_xyhbond_nbd_other 0.048 r_bond_refined_d 0.018 r_bond_other_d 0.01 r_gen_planes_other 0.009 r_gen_planes_refined 0.006 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3927 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction