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Glucocorticoid Receptor DNA Binding Domain in complex with AP-1 response element from VCAM-1 Promoter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.05 M Na Cacodylate (pH 7), 5 mM MgCl2, 1 mM Spermine, and 2 % t-Butanol
Crystal Properties Matthews coefficient Solvent content 3.86 68.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.442 α = 90 b = 96.28 β = 90 c = 105.223 γ = 90
Symmetry Space Group P 21 21 21
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 300 mm CCD 2013-01-13 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 Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.28 50 96.7 0.133 0.145 0.056 7.3 6.9 18797 41.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.36 90.1 0.807 0.877 0.338 0.717 6.7 1723
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 4HN5 2.295 34.483 1.35 17533 1231 94.13 0.1999 0.1974 0.1979 0.2314 0.2317 42.9987
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.335 f_angle_d 0.972 f_chiral_restr 0.049 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1092 Nucleic Acid Atoms 650 Solvent Atoms 42 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction PHENIX phasing HKL-2000 data reduction Coot model building