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Crystal structure of NEMO in complex with Ubv-LIN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F89
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 22.5% polyethylene glycol 3350, 0.1M Magnesium chloride, 0.1M Try-HCl, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.13 60.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.323 α = 90 b = 80.773 β = 90 c = 84.929 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS PILATUS 2M 2020-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 2.6 44.99 100 0.997 10.7 6.6 101221
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 2.6 2.74 0.548
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 3f89 2.6 40.42 13833 1587 99.91 0.2437 0.2384 0.2399 0.2906 0.2902 RANDOM 53.685
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] -2.24 1.81 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.859 r_dihedral_angle_4_deg 20.511 r_dihedral_angle_3_deg 19.145 r_dihedral_angle_1_deg 5.067 r_angle_refined_deg 1.309 r_angle_other_deg 1.124 r_chiral_restr 0.048 r_bond_refined_d 0.01 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.859 r_dihedral_angle_4_deg 20.511 r_dihedral_angle_3_deg 19.145 r_dihedral_angle_1_deg 5.067 r_angle_refined_deg 1.309 r_angle_other_deg 1.124 r_chiral_restr 0.048 r_bond_refined_d 0.01 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2415 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing