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Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR301 and a synthetic peptide containing the NR2 box of DRIP 205
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.25 45.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.188 α = 90 b = 136.344 β = 90 c = 47.29 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 1.99 50 19379
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 MOLECULAR REPLACEMENT THROUGHOUT 1.99 38.87 19379 1044 99.99 0.20843 0.20573 0.2051 0.25764 0.2502 RANDOM 15.172
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.581 r_dihedral_angle_4_deg 15.959 r_dihedral_angle_3_deg 15.087 r_dihedral_angle_1_deg 6.4 r_scangle_it 4.282 r_scbond_it 2.923 r_mcangle_it 1.84 r_angle_refined_deg 1.59 r_mcbond_it 1.268 r_symmetry_vdw_refined 0.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.581 r_dihedral_angle_4_deg 15.959 r_dihedral_angle_3_deg 15.087 r_dihedral_angle_1_deg 6.4 r_scangle_it 4.282 r_scbond_it 2.923 r_mcangle_it 1.84 r_angle_refined_deg 1.59 r_mcbond_it 1.268 r_symmetry_vdw_refined 0.371 r_symmetry_hbond_refined 0.308 r_nbtor_refined 0.307 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2007 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement