☰ Navigation Tabs
Crystal structure of VDR-LBD complexed with 25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
Crystal Properties Matthews coefficient Solvent content 2.16 43.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.74 α = 90 b = 43.16 β = 95.32 c = 42.03 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 2M 2016-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 1.96 32.95 91.9 8.8 2.9 18216
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 1.96 32.95 17130 919 90.9 0.21 0.207 0.2198 0.256 0.2649 RANDOM 35.33
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] -3.08 -1.05 3.62 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.889 r_dihedral_angle_4_deg 23.971 r_dihedral_angle_3_deg 17.658 r_long_range_B_other 7.303 r_long_range_B_refined 7.295 r_dihedral_angle_1_deg 5.598 r_scangle_other 5.303 r_mcangle_it 4.237 r_mcangle_other 4.236 r_scbond_it 3.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.889 r_dihedral_angle_4_deg 23.971 r_dihedral_angle_3_deg 17.658 r_long_range_B_other 7.303 r_long_range_B_refined 7.295 r_dihedral_angle_1_deg 5.598 r_scangle_other 5.303 r_mcangle_it 4.237 r_mcangle_other 4.236 r_scbond_it 3.482 r_scbond_other 3.48 r_mcbond_it 2.863 r_mcbond_other 2.863 r_angle_refined_deg 1.872 r_angle_other_deg 0.884 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2001 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement