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Crystal structure of MINDY-1 tMIU in complex with K48-diUb
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293.15 100 mM sodium acetate pH 5.4 and 18.5 % PEG3350
Crystal Properties Matthews coefficient Solvent content 1.82 32.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.14 α = 90 b = 55.14 β = 90 c = 105.51 γ = 90
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 2M 2015-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96769 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.05 48.87 100 0.043 0.999 19.4 6.6 9899
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.11 100 0.544 0.818 2.9 6.6
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 1UBQ 2.05 48.87 9368 517 99.97 0.18484 0.18268 0.1948 0.22341 0.2296 RANDOM 58.638
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] 0.34 0.34 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.29 r_dihedral_angle_3_deg 14.185 r_dihedral_angle_4_deg 13.893 r_long_range_B_other 7.313 r_long_range_B_refined 7.303 r_scangle_other 6.165 r_dihedral_angle_1_deg 6.1 r_scbond_it 3.95 r_scbond_other 3.947 r_mcangle_other 3.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.29 r_dihedral_angle_3_deg 14.185 r_dihedral_angle_4_deg 13.893 r_long_range_B_other 7.313 r_long_range_B_refined 7.303 r_scangle_other 6.165 r_dihedral_angle_1_deg 6.1 r_scbond_it 3.95 r_scbond_other 3.947 r_mcangle_other 3.808 r_mcangle_it 3.804 r_mcbond_it 3.035 r_mcbond_other 3.014 r_angle_refined_deg 1.441 r_angle_other_deg 0.904 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1332 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction PHASER phasing REFMAC refinement XDS data scaling