☰ Navigation Tabs
Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RK3 PDB ENTRY 1rk3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.2M malonic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.809 α = 90 b = 45.349 β = 100.13 c = 46.662 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 PSI PILATUS 6M 2008-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 2.5 50 99.3 0.095 8.2 3.1 9008 2 1
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) 2.5 2.59 96.4 0.252 3.3 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 1rk3 2.5 40.36 3 9008 8573 434 99.29 0.23282 0.22919 0.225 0.30939 0.3032 RANDOM 27.112
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] 0.02 -0.09 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.319 r_dihedral_angle_4_deg 17.41 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 5.11 r_scangle_it 2.28 r_scbond_it 1.393 r_angle_refined_deg 1.334 r_mcangle_it 0.97 r_mcbond_it 0.56 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.319 r_dihedral_angle_4_deg 17.41 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 5.11 r_scangle_it 2.28 r_scbond_it 1.393 r_angle_refined_deg 1.334 r_mcangle_it 0.97 r_mcbond_it 0.56 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 1965 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing