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Crystal structure of p53 epitope-scaffold based on a inhibitor of cysteine proteases in complex with human MDM2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EQS modified 3EQS and 3M86 experimental model PDB 3M86 modified 3EQS and 3M86
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 0.1 M NaCl
0.1 M HEPES pH 7.5
1.6 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.62 53.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.361 α = 90 b = 87.361 β = 90 c = 160.84 γ = 90
Symmetry Space Group P 43 21 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 MARMOSAIC 225 mm CCD 2015-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.92 61.77 100 0.148 0.16 0.998 9.8 7.3 48192 29.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.97 100 2.201 0.288 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE modified 3EQS and 3M86 1.923 48.989 1.34 48093 2474 99.96 0.2227 0.2213 0.2242 0.2487 0.2494 Random 32.3187
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.945 f_angle_d 0.832 f_chiral_restr 0.033 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2844 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 28
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction iMOSFLM data processing Coot model building iMOSFLM data reduction