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Molecular basis for the inhibition of p53 by Mdmx
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T4F PDB ENTRY 1T4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 280 30% PEG 300, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.08 α = 90 b = 30.54 β = 102.94 c = 101.1 γ = 90
Symmetry Space Group P 1 21 1
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 130 mm mirror 2007-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 2.3 30 93.2 0.093 25273 23555 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) 2.3 2.4 96.3 0.25 5.25
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1T4F 2.3 20 2 2 20789 1117 98.95 0.22 0.21329 0.21052 0.2082 0.26443 0.2597 RANDOM 21.136
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] -0.69 -0.64 -1.02 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.454 r_dihedral_angle_4_deg 20.976 r_dihedral_angle_3_deg 16.737 r_dihedral_angle_1_deg 6.062 r_scangle_it 2.045 r_scbond_it 1.306 r_angle_refined_deg 1.189 r_mcangle_it 0.976 r_mcbond_it 0.573 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.454 r_dihedral_angle_4_deg 20.976 r_dihedral_angle_3_deg 16.737 r_dihedral_angle_1_deg 6.062 r_scangle_it 2.045 r_scbond_it 1.306 r_angle_refined_deg 1.189 r_mcangle_it 0.976 r_mcbond_it 0.573 r_nbtor_refined 0.297 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.188 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2487 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XSCALE data scaling MOLREP phasing