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Crystal structure of Nurr1 binding to NBRE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CIT 1CIT,1OVL experimental model PDB 1OVL 1CIT,1OVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 277 0.1M sodium malonate, pH5.0, 20% PEG3350,1.44% myo-lnositol
Crystal Properties Matthews coefficient Solvent content 2.68 54.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.002 α = 90 b = 124.002 β = 90 c = 119.518 γ = 120
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 PILATUS3 6M 2017-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97775 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.1 119.52 99.7 0.162 0.172 0.056 0.997 7.9 9.6 37212
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.24 99.9 1.102 1.168 0.379 0.642 9.7
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 1CIT,1OVL 3.1 107.39 35419 1762 99.66 0.2254 0.2233 0.2257 0.2671 0.2725 RANDOM 84.256
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] -1.76 -0.88 -1.76 5.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.898 r_dihedral_angle_3_deg 19.625 r_dihedral_angle_4_deg 16.826 r_dihedral_angle_1_deg 6.497 r_angle_refined_deg 1.449 r_angle_other_deg 1.223 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.898 r_dihedral_angle_3_deg 19.625 r_dihedral_angle_4_deg 16.826 r_dihedral_angle_1_deg 6.497 r_angle_refined_deg 1.449 r_angle_other_deg 1.223 r_chiral_restr 0.065 r_bond_refined_d 0.007 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 9908 Nucleic Acid Atoms 2600 Solvent Atoms 28 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing