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Crystal structure of NEMO CoZi in complex with HOIP NZF1 and linear diubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris-HCl, pH 8.5, 22% v/v PEG Smear Broad
Crystal Properties Matthews coefficient Solvent content 2.86 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.95 α = 90 b = 69.56 β = 90 c = 180.05 γ = 90
Symmetry Space Group P 2 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 2021-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 4.2 56.01 99.9 0.83 9.5 13.1 5542
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 4.2 4.7 99.8 0.42 5.8 12.9
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 4owf 4.2 56.01 5239 285 99.77 0.2254 0.2221 0.2236 0.2858 0.2799 RANDOM 90.975
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] 1.3 6.49 -7.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.902 r_dihedral_angle_3_deg 23.522 r_dihedral_angle_4_deg 16.613 r_dihedral_angle_1_deg 8.424 r_angle_refined_deg 1.497 r_angle_other_deg 1.118 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.902 r_dihedral_angle_3_deg 23.522 r_dihedral_angle_4_deg 16.613 r_dihedral_angle_1_deg 8.424 r_angle_refined_deg 1.497 r_angle_other_deg 1.118 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3894 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing