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Crystal Structure of Nur77 LBD in complex with DBIC compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 PEG4000, Sodium citrate, Glycerol
Crystal Properties Matthews coefficient Solvent content 3.3 62.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.522 α = 90 b = 76.094 β = 90 c = 128.273 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2023-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.57 50 95.8 0.78 11.867 3.1 22762
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.61 0.785
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.575 33.36 22023 1075 92.674 0.209 0.2062 0.2091 0.2655 0.2688 42.735
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] 0.478 0.196 -0.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.256 r_dihedral_angle_4_deg 21.524 r_dihedral_angle_3_deg 19.845 r_lrange_it 10.132 r_lrange_other 10.124 r_dihedral_angle_1_deg 5.817 r_scangle_it 5.593 r_scangle_other 5.592 r_mcangle_it 5.139 r_mcangle_other 5.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.256 r_dihedral_angle_4_deg 21.524 r_dihedral_angle_3_deg 19.845 r_lrange_it 10.132 r_lrange_other 10.124 r_dihedral_angle_1_deg 5.817 r_scangle_it 5.593 r_scangle_other 5.592 r_mcangle_it 5.139 r_mcangle_other 5.138 r_scbond_it 3.501 r_scbond_other 3.5 r_mcbond_it 3.248 r_mcbond_other 3.242 r_angle_refined_deg 1.478 r_angle_other_deg 1.229 r_nbd_other 0.243 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.199 r_symmetry_nbd_refined 0.196 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.153 r_ncsr_local_group_1 0.137 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3582 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing