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Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MNJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 0.1 M HEPES, 10 % w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.03 α = 90 b = 153.15 β = 107.01 c = 82.08 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 16M 2017-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.82 52.623 98.1 0.998 13.8 3.4 113701
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 1.82 1.85 0.652
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5MNJ 1.82 52.623 113660 5516 98.025 0.197 0.1949 0.2305 0.2511 48.798
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] -0.827 -0.094 -3.237 3.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.461 r_dihedral_angle_4_deg 15.583 r_dihedral_angle_3_deg 14.674 r_lrange_it 9.507 r_lrange_other 9.491 r_scangle_it 7.754 r_scangle_other 7.753 r_dihedral_angle_1_deg 6.253 r_mcangle_it 5.581 r_mcangle_other 5.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.461 r_dihedral_angle_4_deg 15.583 r_dihedral_angle_3_deg 14.674 r_lrange_it 9.507 r_lrange_other 9.491 r_scangle_it 7.754 r_scangle_other 7.753 r_dihedral_angle_1_deg 6.253 r_mcangle_it 5.581 r_mcangle_other 5.58 r_scbond_it 5.21 r_scbond_other 5.21 r_mcbond_other 4.201 r_mcbond_it 4.2 r_angle_refined_deg 1.462 r_angle_other_deg 1.356 r_nbd_other 0.227 r_symmetry_xyhbond_nbd_refined 0.213 r_nbd_refined 0.197 r_symmetry_nbd_other 0.191 r_symmetry_nbd_refined 0.183 r_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.161 r_ncsr_local_group_13 0.116 r_ncsr_local_group_1 0.114 r_ncsr_local_group_17 0.111 r_ncsr_local_group_11 0.11 r_ncsr_local_group_4 0.106 r_ncsr_local_group_2 0.105 r_ncsr_local_group_16 0.105 r_ncsr_local_group_5 0.103 r_ncsr_local_group_10 0.103 r_ncsr_local_group_12 0.095 r_ncsr_local_group_15 0.093 r_metal_ion_refined 0.091 r_ncsr_local_group_9 0.091 r_ncsr_local_group_18 0.09 r_ncsr_local_group_3 0.088 r_ncsr_local_group_6 0.084 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_14 0.073 r_chiral_restr 0.072 r_ncsr_local_group_7 0.066 r_ncsr_local_group_8 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8781 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing