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Structure of human MDM2 protein in complex with Mi-63-analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 300 0.1M sodium-acetate-trihydrate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.94 α = 90 b = 97.35 β = 90 c = 106.63 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MAR CCD 165 mm monochromator, mirror 2009-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
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 1.6 50 83 0.044 20.45 39422 39422 2 2
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) 1.6 1.7 42.7 0.184 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1YCR 1.6 20 36937 34656 1823 92.53 0.19285 0.19062 0.1952 0.23606 0.2422 RANDOM 15.587
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] -0.04 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.752 r_dihedral_angle_4_deg 18.744 r_dihedral_angle_3_deg 13.954 r_dihedral_angle_1_deg 4.95 r_scangle_it 2.85 r_angle_refined_deg 1.737 r_scbond_it 1.696 r_sphericity_free 1.607 r_mcangle_it 1.244 r_angle_other_deg 0.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.752 r_dihedral_angle_4_deg 18.744 r_dihedral_angle_3_deg 13.954 r_dihedral_angle_1_deg 4.95 r_scangle_it 2.85 r_angle_refined_deg 1.737 r_scbond_it 1.696 r_sphericity_free 1.607 r_mcangle_it 1.244 r_angle_other_deg 0.996 r_rigid_bond_restr 0.831 r_sphericity_bonded 0.792 r_mcbond_it 0.654 r_chiral_restr 0.236 r_mcbond_other 0.15 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2178 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 96
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling