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Crystal Structure of Nur77 LBD in complex with NLM1
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 3.58 65.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.463 α = 90 b = 76.435 β = 90 c = 127.866 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 2022-01-22 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) R Merge 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 2.179 50 100 0.154 24.182 11.4 38870
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 2.179 2.22 0.822
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.179 37.259 38784 1906 99.81 0.241 0.239 0.2738 0.272 48.876
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] 0.408 1.705 -2.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_dihedral_angle_3_deg 19.293 r_dihedral_angle_4_deg 16.823 r_lrange_it 10.217 r_lrange_other 10.216 r_scangle_it 7.218 r_scangle_other 7.217 r_dihedral_angle_1_deg 6.009 r_mcangle_it 5.877 r_mcangle_other 5.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_dihedral_angle_3_deg 19.293 r_dihedral_angle_4_deg 16.823 r_lrange_it 10.217 r_lrange_other 10.216 r_scangle_it 7.218 r_scangle_other 7.217 r_dihedral_angle_1_deg 6.009 r_mcangle_it 5.877 r_mcangle_other 5.875 r_scbond_it 4.949 r_scbond_other 4.948 r_mcbond_it 4.302 r_mcbond_other 4.301 r_angle_refined_deg 1.612 r_angle_other_deg 1.284 r_symmetry_nbd_refined 0.259 r_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.206 r_nbd_other 0.199 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.167 r_ncsr_local_group_1 0.152 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_xyhbond_nbd_other 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3584 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing