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Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human MEp DR1 Response Element, pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 20% PEG 3350, 0.1M MOPS pH 7.0, 0.1M NH4Cl, 0.1M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.27 45.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.333 α = 90 b = 44.257 β = 98.31 c = 62.137 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 PILATUS3 6M 2016-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.2821 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.54 42.44 87.8 0.097 0.123 0.075 0.992 5.5 2.3 35888 22.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 65.3 1.075 1.391 0.875 0.144 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 4CN5 1.6 42.44 32765 1658 88.7 0.164 0.163 0.1663 0.198 0.2011 RANDOM 34.29
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] -2.0783 3.8859 1.1319 0.9464
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.35 t_omega_torsion 3.33 t_angle_deg 1.04 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.35 t_omega_torsion 3.33 t_angle_deg 1.04 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1315 Nucleic Acid Atoms 691 Solvent Atoms 440 Heterogen Atoms 32
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing BUSTER refinement PDB_EXTRACT data extraction