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Co-crystal Structure of MDM2 in Complex with AM-7209
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ERF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 1.4M Ammonium Sulfate, 0.1M Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.59 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.517 α = 90 b = 45.517 β = 90 c = 208.624 γ = 120
Symmetry Space Group P 61 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 CCD ADSC QUANTUM 315 2012-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
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 1.42 50 99.9 0.065 8.8 14.5 25560
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 1.42 1.47 99.4 0.774 11.6 2459
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 4ERF 1.42 38.76 24178 1263 99.89 0.177 0.1762 0.1746 0.1919 0.1914 RANDOM 19.269
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] 0.15 0.15 0.15 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.379 r_dihedral_angle_4_deg 19.925 r_dihedral_angle_3_deg 11.726 r_dihedral_angle_1_deg 5.408 r_angle_other_deg 1.36 r_angle_refined_deg 1.233 r_chiral_restr 0.105 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.379 r_dihedral_angle_4_deg 19.925 r_dihedral_angle_3_deg 11.726 r_dihedral_angle_1_deg 5.408 r_angle_other_deg 1.36 r_angle_refined_deg 1.233 r_chiral_restr 0.105 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 839 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing