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Crystal Structure Analysis of the Csn-B-bounded NUR77 Ligand binding Domain
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 277.15 Crystals of apo-LBD was obtained at 4 degrees Celsius by hanging drop vapor diffusion. The droplets consisted of a 1:1 (v/v) mixture of LBD at 6 mg/ml, and the well solution consisted of 100 mM sodium citrate (pH 4.6), 22% glycerol and 5% PEG4000. Crystals appeared after 24-48 h and were ready for data collection in 7 d.
Crystal Properties Matthews coefficient Solvent content 3.46 64.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.589 α = 90 b = 76.099 β = 90 c = 127.736 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 SDMS 2018-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97930 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 4.45 50 91.2 0.149 0.914 4.514 2.4 4038
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.5 4.58 0.492 0.656
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 3V3E 4.45 33.28 3241 154 70.85 0.2485 0.2457 0.2461 0.3079 0.3042 RANDOM 27.911
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] 8.28 -0.4 -7.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.24 r_dihedral_angle_3_deg 17.841 r_dihedral_angle_4_deg 16.373 r_dihedral_angle_1_deg 5.814 r_angle_other_deg 1.434 r_angle_refined_deg 1.049 r_chiral_restr 0.066 r_bond_other_d 0.011 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.24 r_dihedral_angle_3_deg 17.841 r_dihedral_angle_4_deg 16.373 r_dihedral_angle_1_deg 5.814 r_angle_other_deg 1.434 r_angle_refined_deg 1.049 r_chiral_restr 0.066 r_bond_other_d 0.011 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3634 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing