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Glucocorticoid Receptor with Bound D-prolinamide 11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other homology model generated from PR LBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M MES 6.5, 28% PEG 5K MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.927 α = 90 b = 65.956 β = 103.64 c = 71.528 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 210 2006-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 3 50 99.1 0.079 8.1 3.6 17141 16987 36.7
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 3 3.11 93.2 0.381 2.9 1565
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 (All) 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 homology model generated from PR LBD 3 19.82 16800 16800 1170 100 0.229 0.229 0.224 0.2327 0.289 0.2374 RANDOM 61.285
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] 2.12 -1.8 -3.27 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.149 r_dihedral_angle_3_deg 17.287 r_dihedral_angle_4_deg 14.544 r_dihedral_angle_1_deg 5.341 r_angle_refined_deg 1.243 r_scangle_it 0.915 r_angle_other_deg 0.85 r_mcangle_it 0.638 r_scbond_it 0.589 r_mcbond_it 0.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.149 r_dihedral_angle_3_deg 17.287 r_dihedral_angle_4_deg 14.544 r_dihedral_angle_1_deg 5.341 r_angle_refined_deg 1.243 r_scangle_it 0.915 r_angle_other_deg 0.85 r_mcangle_it 0.638 r_scbond_it 0.589 r_mcbond_it 0.579 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.223 r_symmetry_hbond_refined 0.194 r_nbtor_refined 0.192 r_nbd_other 0.186 r_symmetry_vdw_other 0.176 r_xyhbond_nbd_other 0.159 r_xyhbond_nbd_refined 0.156 r_nbtor_other 0.088 r_chiral_restr 0.053 r_mcbond_other 0.049 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5970 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 141
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling