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Crystal structure of the N-terminal 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 2.09 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.552 α = 90 b = 47.552 β = 90 c = 90.676 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 2020-01-01 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 11624
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 1.632 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6Q9W, 6V4F 1.632 42.148 11624 563 85.584 0.201 0.2 0.2269 0.2394 35.876
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] 0.018 0.018 -0.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.735 r_dihedral_angle_4_deg 16.874 r_dihedral_angle_3_deg 15.581 r_lrange_it 8.506 r_lrange_other 8.502 r_dihedral_angle_1_deg 6.887 r_scangle_it 6.807 r_scangle_other 6.802 r_mcangle_other 4.457 r_mcangle_it 4.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.735 r_dihedral_angle_4_deg 16.874 r_dihedral_angle_3_deg 15.581 r_lrange_it 8.506 r_lrange_other 8.502 r_dihedral_angle_1_deg 6.887 r_scangle_it 6.807 r_scangle_other 6.802 r_mcangle_other 4.457 r_mcangle_it 4.446 r_scbond_it 4.432 r_scbond_other 4.428 r_mcbond_it 3.116 r_mcbond_other 3.087 r_angle_other_deg 2.177 r_angle_refined_deg 1.632 r_symmetry_xyhbond_nbd_refined 0.26 r_nbd_refined 0.212 r_symmetry_nbd_other 0.212 r_nbd_other 0.199 r_symmetry_nbd_refined 0.187 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.077 r_bond_other_d 0.034 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 773 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 58
Software Software Software Name Purpose HKL-2000 data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction