☰ Navigation Tabs
Vitamin D3 receptor/lithochoric acid derivative complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M MOPS-NaOH (pH 7.0), 0.2 M sodium formate, 12% (w/v) PEG4000, and 8% (v/v) ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.85 33.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.144 α = 90 b = 37.436 β = 98.581 c = 40.91 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 95 PIXEL DECTRIS PILATUS3 6M 2015-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.9 40 98.6 0.069 0.998 9.9 3.2 18622
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.02 95.7 0.763 0.783 2.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZLC 1.9 40 18617 937 98.644 0.194 0.1912 0.1912 0.248 0.248 39.447
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] -3.413 -1.368 1.451 2.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.715 r_dihedral_angle_3_deg 14.764 r_dihedral_angle_4_deg 13.628 r_lrange_it 7.984 r_lrange_other 7.984 r_scangle_it 6.302 r_scangle_other 6.3 r_dihedral_angle_1_deg 5.516 r_mcangle_it 4.374 r_mcangle_other 4.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.715 r_dihedral_angle_3_deg 14.764 r_dihedral_angle_4_deg 13.628 r_lrange_it 7.984 r_lrange_other 7.984 r_scangle_it 6.302 r_scangle_other 6.3 r_dihedral_angle_1_deg 5.516 r_mcangle_it 4.374 r_mcangle_other 4.372 r_scbond_it 4.159 r_scbond_other 4.156 r_mcbond_it 3.041 r_mcbond_other 3.04 r_angle_refined_deg 1.532 r_angle_other_deg 1.332 r_symmetry_nbd_refined 0.243 r_nbd_refined 0.212 r_symmetry_nbd_other 0.166 r_nbtor_refined 0.163 r_nbd_other 0.163 r_symmetry_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1927 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing