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Crystal structure of the p53-binding domain of human MdmX protein in complex with Nutlin3a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q9W 6Q9W, 6V4F experimental model PDB 6V4F 6Q9W, 6V4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20% v/v Tacsimate pH 7.0, 0.1 M HEPES sodium salt pH 7.5, 2% (w/v) PEG 200
Crystal Properties Matthews coefficient Solvent content 2.33 47.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.47 α = 90 b = 47.47 β = 90 c = 91.19 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER X 16M 2020-01-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.632 42.148 100 0.06 0.062 0.013 1 28.4 22.7 13154
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.94 100 0.854 0.882 0.215 0.884 16.4
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 6Q9W, 6V4F 1.65 25.611 13154 675 99.75 0.21 0.2075 0.2074 0.2647 0.2638 36.364
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] 0.715 0.715 -1.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.691 r_dihedral_angle_4_deg 24.958 r_dihedral_angle_3_deg 15.726 r_lrange_it 8.018 r_lrange_other 8.014 r_dihedral_angle_1_deg 7.156 r_scangle_other 6.798 r_scangle_it 6.57 r_scbond_it 4.648 r_scbond_other 4.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.691 r_dihedral_angle_4_deg 24.958 r_dihedral_angle_3_deg 15.726 r_lrange_it 8.018 r_lrange_other 8.014 r_dihedral_angle_1_deg 7.156 r_scangle_other 6.798 r_scangle_it 6.57 r_scbond_it 4.648 r_scbond_other 4.643 r_mcangle_it 4.224 r_mcangle_other 4.22 r_mcbond_it 3.173 r_mcbond_other 3.138 r_angle_other_deg 2.195 r_angle_refined_deg 1.699 r_nbd_refined 0.225 r_symmetry_nbd_other 0.222 r_nbd_other 0.188 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.178 r_symmetry_nbd_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.083 r_bond_other_d 0.034 r_gen_planes_other 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 773 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 58
Software Software Software Name Purpose HKL-2000 data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction