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Crystal structure of the computationally designed chemically disruptable heterodimer LD6-MDM2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AFG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.5 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.15 42.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.238 α = 90 b = 73.238 β = 90 c = 92.262 γ = 90
Symmetry Space Group P 43 2 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 PILATUS 2M-F 2018-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 2.95 45.2 99.8 0.99 22.18 6.9 5646
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 2.95 3.13 99.8 0.67 2.19
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 (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 5AFG 2.95 45.2 5361 285 99.81 0.2006 0.1971 0.201 0.2599 0.2586 RANDOM 86.097
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] 1.95 1.95 -3.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.781 r_dihedral_angle_3_deg 22.783 r_dihedral_angle_4_deg 14.692 r_dihedral_angle_1_deg 7.858 r_angle_refined_deg 1.61 r_angle_other_deg 1.216 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.781 r_dihedral_angle_3_deg 22.783 r_dihedral_angle_4_deg 14.692 r_dihedral_angle_1_deg 7.858 r_angle_refined_deg 1.61 r_angle_other_deg 1.216 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1656 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing