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Crystal structure of the ligand binding domain of polyandrocarpa misakiensis rxr in tetramer in absence of ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XDK RXR part of PDB ENTRY 1XDK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1M Pipes. 17% Peg 4K. 15mM Sodium chloride. 1mM n-dodecyl B-D-maltoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.26 α = 90 b = 96.12 β = 90 c = 151.72 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 MAR CCD 165 mm 2005-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9794 ESRF BM30A
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 2.9 48.224 99.5 0.071 18.51 5.26 27360 27210 -3 55.294
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 2.9 3 98.6 0.409 4.4 5.22 2560
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 (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 RXR part of PDB ENTRY 1XDK 2.9 48.22 27210 27207 1361 100 0.272 0.269 0.2685 0.325 0.3306 RANDOM 59.075
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] -2.9 4.66 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.78 r_dihedral_angle_4_deg 19.825 r_dihedral_angle_3_deg 15.518 r_dihedral_angle_1_deg 5.498 r_angle_refined_deg 1.003 r_angle_other_deg 0.762 r_mcangle_it 0.532 r_scangle_it 0.34 r_mcbond_it 0.291 r_scbond_it 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.78 r_dihedral_angle_4_deg 19.825 r_dihedral_angle_3_deg 15.518 r_dihedral_angle_1_deg 5.498 r_angle_refined_deg 1.003 r_angle_other_deg 0.762 r_mcangle_it 0.532 r_scangle_it 0.34 r_mcbond_it 0.291 r_scbond_it 0.2 r_nbd_refined 0.187 r_nbtor_refined 0.168 r_nbd_other 0.162 r_xyhbond_nbd_refined 0.111 r_symmetry_vdw_other 0.106 r_nbtor_other 0.08 r_symmetry_vdw_refined 0.062 r_chiral_restr 0.056 r_mcbond_other 0.02 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6081 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction