☰ Navigation Tabs
Crystal structure of Platynereis dumerilii RAR ligand-binding domain in complex with all-trans retinoic acid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M sodium acetate, 0.1 M HEPES pH 7.5, 20% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.72 54.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.41 α = 90 b = 68.15 β = 100.75 c = 95.08 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 PIXEL DECTRIS PILATUS 6M 2013-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.69 50 98.8 0.053 0.064 0.035 17.6 3.2 32596
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.78 99.7 0.589 0.589 0.697 0.369 1.3 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.69 50 30964 1633 98.58 0.2573 0.2551 0.2634 0.2997 0.3097 RANDOM 52.951
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] 2.17 -2.29 -2.2 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.542 r_dihedral_angle_4_deg 28.434 r_dihedral_angle_3_deg 25.517 r_dihedral_angle_1_deg 7.216 r_angle_refined_deg 2.23 r_chiral_restr 0.146 r_bond_refined_d 0.019 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7069 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 44
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MoRDa phasing