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Vitamin D receptor with a synthetic ligand ADRO2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W5P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M MOPS/NaOH, 0.2M sodium formate, 14-18%(w/v) PEG4000, 8% (v/v) ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.09 41.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.665 α = 90 b = 41.763 β = 95.58 c = 42.01 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 CCD ADSC QUANTUM 270 2015-06-17 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) 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 50 99.2 0.078 7.6 3.2 18042
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.4 0.685 1.3 3.3
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 3W5P 2 50.01 17148 901 99.14 0.19683 0.19432 0.2019 0.24338 0.2446 RANDOM 50.249
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] -4.09 -2.36 2.07 2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.492 r_dihedral_angle_4_deg 20.11 r_dihedral_angle_3_deg 17.532 r_long_range_B_other 9.1 r_long_range_B_refined 9.077 r_scangle_other 7.357 r_dihedral_angle_1_deg 5.95 r_mcangle_other 5.718 r_mcangle_it 5.712 r_scbond_it 4.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.492 r_dihedral_angle_4_deg 20.11 r_dihedral_angle_3_deg 17.532 r_long_range_B_other 9.1 r_long_range_B_refined 9.077 r_scangle_other 7.357 r_dihedral_angle_1_deg 5.95 r_mcangle_other 5.718 r_mcangle_it 5.712 r_scbond_it 4.943 r_scbond_other 4.941 r_mcbond_it 4.045 r_mcbond_other 4.02 r_angle_refined_deg 1.897 r_angle_other_deg 1.061 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 2004 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing