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X-ray Crystal Structure of AncGR2 in Complex with Dexamethasone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q1H PDB entry 2Q1H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 0.5-0.75M ammonium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.63 66.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.218 α = 90 b = 104.218 β = 90 c = 144.166 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 100 IMAGE PLATE MAR scanner 300 mm plate Double Crystal Monochromator Si-220 2008-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 100 0.115 7.3 30813 30813 52.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 100 0.44 5.2 7.3 3879
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2Q1H 2.5 49.01 29216 1550 99.98 0.19888 0.1959 0.1948 0.25467 0.2518 RANDOM 39.643
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] 0.38 0.19 0.38 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.805 r_dihedral_angle_3_deg 19.753 r_dihedral_angle_4_deg 17.842 r_dihedral_angle_1_deg 5.312 r_rigid_bond_restr 4.17 r_scbond_it 3.979 r_sphericity_free 3.867 r_scangle_it 3.507 r_sphericity_bonded 2.404 r_mcangle_it 1.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.805 r_dihedral_angle_3_deg 19.753 r_dihedral_angle_4_deg 17.842 r_dihedral_angle_1_deg 5.312 r_rigid_bond_restr 4.17 r_scbond_it 3.979 r_sphericity_free 3.867 r_scangle_it 3.507 r_sphericity_bonded 2.404 r_mcangle_it 1.499 r_angle_refined_deg 1.434 r_mcbond_it 0.895 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.157 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4213 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 56
Software Software Software Name Purpose SERGUI data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling