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Human Retinoic acid receptor RXR-gamma ligand-binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 300 peg, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.32 47.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.07 α = 90 b = 161.316 β = 109.5 c = 68.682 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 315 2006-03-20 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) 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 2.4 80.58 99.1 37858 37858
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 93.9
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 1RDT 2.4 80.58 36107 36107 1936 98.99 0.24528 0.24528 0.24266 0.2419 0.29574 0.2944 RANDOM 62.588
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] -0.23 -1.11 -1.27 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.284 r_dihedral_angle_4_deg 19.87 r_dihedral_angle_3_deg 18.054 r_dihedral_angle_1_deg 6.696 r_scangle_it 2.218 r_angle_refined_deg 1.475 r_scbond_it 1.384 r_mcangle_it 1.016 r_mcbond_it 0.577 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.284 r_dihedral_angle_4_deg 19.87 r_dihedral_angle_3_deg 18.054 r_dihedral_angle_1_deg 6.696 r_scangle_it 2.218 r_angle_refined_deg 1.475 r_scbond_it 1.384 r_mcangle_it 1.016 r_mcbond_it 0.577 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.281 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.107 r_symmetry_hbond_refined 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5811 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction DENZO data reduction SCALEPACK data scaling MOLREP phasing