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Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediated by conjugate addition and cyclization
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 293 0.1 M MOPS-Na pH 7.0, 0.1 M sodium formate, 15% PEG4000, 5% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.17 43.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.93 α = 90 b = 43.39 β = 95.3 c = 42 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 CCD ADSC QUANTUM 270 2018-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.3 41.75 98.9 0.047 0.029 0.997 23.2 3.6 12346
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.39 0.109 0.066 0.989
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 2ZLC 2.3 29.18 11749 592 98.73 0.20486 0.20234 0.2084 0.25594 0.266 RANDOM 32.774
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] -0.34 0.08 -0.09 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.273 r_dihedral_angle_4_deg 21.161 r_dihedral_angle_3_deg 17.132 r_dihedral_angle_1_deg 5.768 r_long_range_B_refined 3.625 r_long_range_B_other 3.625 r_scangle_other 2.347 r_mcangle_it 1.989 r_mcangle_other 1.989 r_angle_refined_deg 1.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.273 r_dihedral_angle_4_deg 21.161 r_dihedral_angle_3_deg 17.132 r_dihedral_angle_1_deg 5.768 r_long_range_B_refined 3.625 r_long_range_B_other 3.625 r_scangle_other 2.347 r_mcangle_it 1.989 r_mcangle_other 1.989 r_angle_refined_deg 1.705 r_scbond_it 1.485 r_scbond_other 1.484 r_mcbond_it 1.235 r_mcbond_other 1.235 r_angle_other_deg 0.877 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 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 1998 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling REFMAC phasing