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CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH 12-MER PEPTIDE INHIBITOR M3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M sodium cacodylate pH 5.5, 25% PEG (w/v) 4000
Crystal Properties Matthews coefficient Solvent content 1.84 33.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.567 α = 90 b = 87.895 β = 92.3 c = 36.576 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 PSI PILATUS 6M 2016-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.65 43.95 96.4 0.866 1.09 3.2 19635
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 3IWY 1.65 43.95 18598 1012 96.4 0.18052 0.17795 0.1886 0.23112 0.2414 RANDOM 32.574
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] -1.29 1.19 -1.82 3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.183 r_dihedral_angle_4_deg 23.709 r_dihedral_angle_3_deg 16.908 r_dihedral_angle_1_deg 6.811 r_long_range_B_refined 5.766 r_long_range_B_other 5.752 r_scangle_other 4.412 r_scbond_it 2.825 r_scbond_other 2.823 r_angle_refined_deg 2.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.183 r_dihedral_angle_4_deg 23.709 r_dihedral_angle_3_deg 16.908 r_dihedral_angle_1_deg 6.811 r_long_range_B_refined 5.766 r_long_range_B_other 5.752 r_scangle_other 4.412 r_scbond_it 2.825 r_scbond_other 2.823 r_angle_refined_deg 2.379 r_mcangle_other 2.352 r_mcangle_it 2.351 r_mcbond_it 1.685 r_mcbond_other 1.678 r_angle_other_deg 1.241 r_chiral_restr 0.161 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1572 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PHASER phasing HKL-2000 data scaling HKL-2000 data reduction