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Progesterone Receptor Ligand Binding Domain with bound Norethindrone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A28
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 PEG 1000, Li2SO4. hepes pH 6.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal Properties Matthews coefficient Solvent content 2.14 42.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.753 α = 90 b = 64.142 β = 95.84 c = 70.138 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 ADSC QUANTUM 210 mirrors 2002-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 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 1.451 20 99.3 0.053 20.1 3.5 63827 54571 2 18
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 1A28 1.451 19.8 63827 63827 4924 100 0.1885 0.18848 0.18637 0.1897 0.21586 0.1864 RANDOM 25.422
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] -0.03 0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.207 r_scangle_it 5.79 r_dihedral_angle_1_deg 4.015 r_scbond_it 3.851 r_mcangle_it 2.576 r_angle_refined_deg 2.16 r_mcbond_it 1.522 r_symmetry_hbond_refined 1.087 r_symmetry_vdw_refined 1.01 r_nbd_refined 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.207 r_scangle_it 5.79 r_dihedral_angle_1_deg 4.015 r_scbond_it 3.851 r_mcangle_it 2.576 r_angle_refined_deg 2.16 r_mcbond_it 1.522 r_symmetry_hbond_refined 1.087 r_symmetry_vdw_refined 1.01 r_nbd_refined 0.239 r_chiral_restr 0.228 r_xyhbond_nbd_refined 0.145 r_bond_refined_d 0.03 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3967 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 44
Software Software Software Name Purpose ADSC data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement