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Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain complexed with Burned Meat Compound 4-OH-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 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.2M Magnesium chloride hexahydrate, 0.1M Tris 8.5, 25% Polyehtlyene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.081 α = 90 b = 84.044 β = 108.85 c = 58.668 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 0.97946 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 1.85 15 95.1 0.064 0.064 17.5 4.3 41792 41792 33.7
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 1.85 1.92 71.2 0.283 0.283 3.68 2.5 3122
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3ERD 1.85 14.99 41769 41769 2117 95 0.171 0.169 0.225 0.2675 RANDOM 21.827
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] -0.02 0.01 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.306 r_dihedral_angle_4_deg 22.726 r_dihedral_angle_3_deg 15.895 r_dihedral_angle_1_deg 5.359 r_scangle_it 3.328 r_scbond_it 2.171 r_mcangle_it 1.503 r_angle_refined_deg 1.422 r_mcbond_it 0.988 r_angle_other_deg 0.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.306 r_dihedral_angle_4_deg 22.726 r_dihedral_angle_3_deg 15.895 r_dihedral_angle_1_deg 5.359 r_scangle_it 3.328 r_scbond_it 2.171 r_mcangle_it 1.503 r_angle_refined_deg 1.422 r_mcbond_it 0.988 r_angle_other_deg 0.957 r_symmetry_vdw_refined 0.33 r_symmetry_vdw_other 0.289 r_symmetry_hbond_refined 0.248 r_nbd_refined 0.24 r_mcbond_other 0.213 r_nbd_other 0.194 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.18 r_nbtor_other 0.091 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3944 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 36
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction