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Crystal Structure of HdmX bound to the p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-6-Cl-Trp-Glu-Ac3c-Leu-NH2 at 1.33A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FE7 PDB ENTRY 3FE7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 3.1M AmSo4, 1% MPD, 0.1M MES, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.249 α = 90 b = 42.249 β = 90 c = 70.449 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 2007-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.98371 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 1.33 20 97.1 0.062 39.165 8.1 27490
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) 1.33 1.38 74.2 0.266 2.1 2078
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 3FE7 1.33 20 27453 1388 96.8 0.194 0.193 0.1924 0.206 0.2042 RANDOM 21.503
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 r_dihedral_angle_2_deg 42.675 r_dihedral_angle_4_deg 21.456 r_dihedral_angle_3_deg 10.674 r_dihedral_angle_1_deg 6.453 r_scangle_it 4.154 r_scbond_it 2.644 r_mcangle_it 1.894 r_angle_refined_deg 1.584 r_mcbond_it 1.007 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.675 r_dihedral_angle_4_deg 21.456 r_dihedral_angle_3_deg 10.674 r_dihedral_angle_1_deg 6.453 r_scangle_it 4.154 r_scbond_it 2.644 r_mcangle_it 1.894 r_angle_refined_deg 1.584 r_mcbond_it 1.007 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 840 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing