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Crystal structure of IsdB linker-NEAT2 bound to a nanobody (VHH)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XLD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 25% PEG 3,350
0.1 M HEPES (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 1.96 37.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.321 α = 90 b = 48.58 β = 90 c = 140.7 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 PILATUS3 6M 2019-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 40 99.8 0.068 0.025 0.998 14.7 8.4 31303
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 0.828 0.325 0.827 2.3
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 7XLD 1.7 40 29982 1251 99.73 0.21 0.2088 0.2139 0.2373 0.2347 RANDOM 42.314
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] 1.93 0.33 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.242 r_dihedral_angle_4_deg 21.751 r_dihedral_angle_1_deg 15.544 r_dihedral_angle_3_deg 14.44 r_angle_refined_deg 1.78 r_angle_other_deg 1.391 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.242 r_dihedral_angle_4_deg 21.751 r_dihedral_angle_1_deg 15.544 r_dihedral_angle_3_deg 14.44 r_angle_refined_deg 1.78 r_angle_other_deg 1.391 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1888 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing