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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 6.5 291 0.1 M HEPES sodium salt pH 7.5, 1.6 M Ammonium sulfate, 2%(w/v) PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.38 48.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.727 α = 90 b = 47.727 β = 90 c = 92.321 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 1.8 42.433 95.9 0.074 0.076 0.015 0.999 25.4 23 10064
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 1.8 1.9 92.1 0.968 1.001 0.244 0.838 15.4
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 1.801 42.433 10024 482 95.804 0.199 0.1967 0.1966 0.2413 0.2405 31.715
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] 0.409 0.409 -0.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.432 r_dihedral_angle_4_deg 16.518 r_dihedral_angle_3_deg 14.524 r_lrange_other 7.935 r_lrange_it 7.934 r_dihedral_angle_1_deg 6.42 r_scangle_it 6.381 r_scangle_other 6.376 r_scbond_it 4.092 r_mcangle_it 4.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.432 r_dihedral_angle_4_deg 16.518 r_dihedral_angle_3_deg 14.524 r_lrange_other 7.935 r_lrange_it 7.934 r_dihedral_angle_1_deg 6.42 r_scangle_it 6.381 r_scangle_other 6.376 r_scbond_it 4.092 r_mcangle_it 4.091 r_scbond_other 4.088 r_mcangle_other 4.087 r_mcbond_it 2.911 r_mcbond_other 2.895 r_angle_other_deg 2.183 r_angle_refined_deg 1.605 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.213 r_symmetry_nbd_other 0.208 r_nbd_other 0.2 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.081 r_bond_other_d 0.033 r_gen_planes_other 0.013 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 20 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction