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Crystal Structure of Nur77 LBD in complex with N-(2'-(4-hydroxypiperidin-1-yl)-[4,4'-bipyridin]-2-yl)cinnamamide
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 3.46 64.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.781 α = 90 b = 76.125 β = 90 c = 128.813 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 0.9792 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 2.68 50 99.9 0.893 4.556 6.4 21249
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 2.68 2.73 0.898
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 2.683 33.944 21189 1069 99.802 0.206 0.2042 0.208 0.2425 0.2467 39.167
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] -0.108 0.396 -0.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.928 r_dihedral_angle_3_deg 19.938 r_dihedral_angle_4_deg 17.522 r_lrange_it 11.382 r_lrange_other 11.378 r_dihedral_angle_1_deg 6.256 r_scangle_it 6.089 r_scangle_other 6.088 r_mcangle_it 5.51 r_mcangle_other 5.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.928 r_dihedral_angle_3_deg 19.938 r_dihedral_angle_4_deg 17.522 r_lrange_it 11.382 r_lrange_other 11.378 r_dihedral_angle_1_deg 6.256 r_scangle_it 6.089 r_scangle_other 6.088 r_mcangle_it 5.51 r_mcangle_other 5.509 r_scbond_it 3.837 r_scbond_other 3.836 r_mcbond_it 3.449 r_mcbond_other 3.442 r_angle_refined_deg 1.573 r_angle_other_deg 1.258 r_nbd_other 0.228 r_nbd_refined 0.227 r_symmetry_nbd_other 0.184 r_symmetry_nbd_refined 0.182 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.153 r_xyhbond_nbd_refined 0.149 r_ncsr_local_group_1 0.13 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.057 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3621 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing