☰ Navigation Tabs
Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other MDM2-E2-Ub complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 292 0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
Crystal Properties Matthews coefficient Solvent content 2.65 53.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.531 α = 90 b = 129.531 β = 90 c = 70.751 γ = 120
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 PILATUS 6M-F 2018-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.559 70.75 100 0.999 13.8 17.3 95993
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 1.56 1.59 0.518
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE MDM2-E2-Ub complex 1.559 70.75 95993 4694 99.803 0.136 0.1335 0.1332 0.1848 0.1845 20.479
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] 0.232 0.116 0.232 -0.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.614 r_dihedral_angle_4_deg 16.235 r_dihedral_angle_3_deg 12.743 r_rigid_bond_restr 7.877 r_dihedral_angle_1_deg 6.655 r_lrange_other 5.478 r_lrange_it 5.476 r_scangle_it 5.266 r_scangle_other 5.265 r_scbond_other 4.627
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.614 r_dihedral_angle_4_deg 16.235 r_dihedral_angle_3_deg 12.743 r_rigid_bond_restr 7.877 r_dihedral_angle_1_deg 6.655 r_lrange_other 5.478 r_lrange_it 5.476 r_scangle_it 5.266 r_scangle_other 5.265 r_scbond_other 4.627 r_scbond_it 4.626 r_mcangle_it 3.615 r_mcangle_other 3.615 r_mcbond_other 2.989 r_mcbond_it 2.988 r_angle_refined_deg 1.773 r_angle_other_deg 1.692 r_nbd_refined 0.233 r_nbd_other 0.223 r_symmetry_nbd_other 0.211 r_symmetry_nbd_refined 0.2 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.168 r_ncsr_local_group_2 0.12 r_chiral_restr 0.098 r_ncsr_local_group_3 0.081 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_1 0.078 r_metal_ion_refined 0.024 r_bond_other_d 0.017 r_bond_refined_d 0.015 r_gen_planes_other 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4513 Nucleic Acid Atoms Solvent Atoms 662 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing