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human MDM2 complex with stapled foldamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EQS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 290 Ammonium Sulfate 2.5M + MES 0.1M pH5.5
Crystal Properties Matthews coefficient Solvent content 2.48 50.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.565 α = 90 b = 109.557 β = 96.97 c = 58.713 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 EIGER X 16M 2021-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978566 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.84 34.57 99.2 0.0715 8.53 2.64 224410
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.94 98 0.5679 2.49
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.841 34.57 42753 2059 99.6 0.2023 0.2004 0.1926 0.2394 0.2336 RANDOM 33.03
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] -0.1339 -0.0547 0.205 -0.0711
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.11 t_omega_torsion 3.65 t_angle_deg 0.9 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3110 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 435
Software Software Software Name Purpose BUSTER refinement XDS data reduction XDS data scaling PHASER phasing