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Crystal structure of Zebrafish MDM2 RING domain homodimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 0.1 M imidazole, 0.12 M monosaccharides, 37.5 % (w/v) MPD_P1K_P3350 (Morpheus, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.25 45.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.163 α = 90 b = 23.859 β = 101.664 c = 54.306 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 2017-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.872 53.185 100 0.949 6.3 3.2 2814
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 2.872 2.922 0.667
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 2VJF 2.872 45.21 2813 172 99.858 0.211 0.2065 0.2082 0.2811 0.2807 23.532
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] 4.54 0.157 -1.29 -3.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.676 r_dihedral_angle_3_deg 19.754 r_dihedral_angle_4_deg 18.407 r_dihedral_angle_1_deg 5.462 r_lrange_it 3.91 r_lrange_other 3.87 r_mcangle_it 2.149 r_mcangle_other 2.147 r_scangle_other 1.993 r_scangle_it 1.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.676 r_dihedral_angle_3_deg 19.754 r_dihedral_angle_4_deg 18.407 r_dihedral_angle_1_deg 5.462 r_lrange_it 3.91 r_lrange_other 3.87 r_mcangle_it 2.149 r_mcangle_other 2.147 r_scangle_other 1.993 r_scangle_it 1.992 r_angle_refined_deg 1.429 r_mcbond_other 1.269 r_mcbond_it 1.268 r_scbond_it 1.241 r_scbond_other 1.24 r_angle_other_deg 1.085 r_symmetry_nbd_refined 0.205 r_symmetry_nbd_other 0.193 r_nbd_refined 0.184 r_nbd_other 0.182 r_xyhbond_nbd_refined 0.157 r_nbtor_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.113 r_ncsr_local_group_1 0.104 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.052 r_metal_ion_refined 0.046 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 868 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing