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Mdm2 in complex with a D amino Acid Containing Stapled Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20 % w/v Polyethylene glycol 8,000, 100 mM HEPES pH 7.5, 200 mM Ammonium sulfate, 10 % v/v 2-Propanol
Crystal Properties Matthews coefficient Solvent content 1.93 36.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.946 α = 90 b = 43.378 β = 94.82 c = 34.542 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 210r 2017-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95372 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 40.33 99.3 0.246 0.267 0.105 5.7 6.3 8132
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 95.2 1.211 1.324 0.528 3.4 5.8
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 4umn 2 40.33 7710 422 99.27 0.18637 0.18412 0.1922 0.22336 0.2294 RANDOM 26.041
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] -0.55 -1.4 0.08 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.023 r_dihedral_angle_4_deg 24.467 r_dihedral_angle_3_deg 14.541 r_dihedral_angle_1_deg 5.947 r_long_range_B_refined 5.768 r_long_range_B_other 5.701 r_scangle_other 3.608 r_mcangle_it 2.794 r_mcangle_other 2.793 r_angle_refined_deg 2.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.023 r_dihedral_angle_4_deg 24.467 r_dihedral_angle_3_deg 14.541 r_dihedral_angle_1_deg 5.947 r_long_range_B_refined 5.768 r_long_range_B_other 5.701 r_scangle_other 3.608 r_mcangle_it 2.794 r_mcangle_other 2.793 r_angle_refined_deg 2.202 r_scbond_it 2.126 r_scbond_other 2.124 r_mcbond_it 1.753 r_mcbond_other 1.747 r_angle_other_deg 1.087 r_chiral_restr 0.347 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 839 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PARROT phasing