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Crystal Structure of HdmX bound to the p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-Trp-Glu-Ac3c-Leu-NH2 at 1.35A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GV2 PDB ENTRY 2GV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 3.1M AmSo4, 1% MPD, 4% polypropyleneglycol, 0.1M MES, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.49 50.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.294 α = 90 b = 43.294 β = 90 c = 65.59 γ = 90
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 MARRESEARCH 2007-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99975 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 1.35 20 94.9 0.057 32.852 6.9 25341
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) 1.35 1.4 61.3 0.266 1.6 1647
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 PDB ENTRY 2GV2 1.35 20 25273 1278 95.16 0.192 0.192 0.1921 0.209 0.2091 RANDOM 16.964
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] -0.11 -0.11 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.738 r_dihedral_angle_4_deg 19.477 r_dihedral_angle_3_deg 11.012 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.954 r_scbond_it 2.527 r_mcangle_it 1.587 r_angle_refined_deg 1.212 r_mcbond_it 1.01 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.738 r_dihedral_angle_4_deg 19.477 r_dihedral_angle_3_deg 11.012 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.954 r_scbond_it 2.527 r_mcangle_it 1.587 r_angle_refined_deg 1.212 r_mcbond_it 1.01 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.203 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 752 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction