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Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other MDM2-E2-Ub
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
Crystal Properties Matthews coefficient Solvent content 2.26 45.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.267 α = 90 b = 80.687 β = 90 c = 135.909 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 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 2.07 135.91 100 0.997 9 6.4 38548
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 2.07 2.11 0.584
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 2.07 69.478 38312 1887 99.517 0.215 0.2121 0.2129 0.266 0.2665 32.5
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] -1.177 -0.078 1.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.601 r_dihedral_angle_4_deg 17.085 r_dihedral_angle_3_deg 14.648 r_dihedral_angle_1_deg 7.481 r_lrange_it 6.61 r_lrange_other 6.609 r_scangle_it 4.682 r_scangle_other 4.681 r_mcangle_it 3.794 r_mcangle_other 3.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.601 r_dihedral_angle_4_deg 17.085 r_dihedral_angle_3_deg 14.648 r_dihedral_angle_1_deg 7.481 r_lrange_it 6.61 r_lrange_other 6.609 r_scangle_it 4.682 r_scangle_other 4.681 r_mcangle_it 3.794 r_mcangle_other 3.794 r_scbond_it 3.022 r_scbond_other 3.021 r_mcbond_it 2.574 r_mcbond_other 2.574 r_angle_refined_deg 1.434 r_angle_other_deg 1.26 r_symmetry_nbd_refined 0.199 r_nbd_refined 0.191 r_symmetry_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.186 r_nbd_other 0.168 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.158 r_ncsr_local_group_1 0.118 r_ncsr_local_group_2 0.104 r_metal_ion_refined 0.098 r_symmetry_nbtor_other 0.09 r_ncsr_local_group_3 0.076 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4458 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing