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Crystal structure of UFC1 in complex with UBA5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride
Crystal Properties Matthews coefficient Solvent content 2.13 42.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.204 α = 90 b = 67.421 β = 90 c = 133.984 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 298 PIXEL DECTRIS PILATUS 6M-F 2018-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9720 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.95 33.71 46.5 0.132 0.999 11.7 8.3 15162 49.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.05 3 1.87 0.478 6.8
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 (All) 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 NONE 2Z6O 1.95 23.761 15105 814 47.144 0.219 0.2185 0.2146 0.215 0.2801 0.2861 Random selection 59.743
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] 0.059 0.502 -0.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.06 r_dihedral_angle_3_deg 20.332 r_dihedral_angle_4_deg 20.26 r_lrange_it 12.708 r_scangle_it 9.175 r_mcangle_it 7.197 r_dihedral_angle_1_deg 6.308 r_scbond_it 6.059 r_mcbond_it 4.702 r_angle_refined_deg 1.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.06 r_dihedral_angle_3_deg 20.332 r_dihedral_angle_4_deg 20.26 r_lrange_it 12.708 r_scangle_it 9.175 r_mcangle_it 7.197 r_dihedral_angle_1_deg 6.308 r_scbond_it 6.059 r_mcbond_it 4.702 r_angle_refined_deg 1.555 r_nbtor_refined 0.311 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.125 r_symmetry_xyhbond_nbd_refined 0.117 r_ncsr_local_group_2 0.117 r_chiral_restr 0.112 r_ncsr_local_group_1 0.107 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2902 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing