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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
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 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.52 α = 90 b = 30.44 β = 102.47 c = 100.85 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 2007-02-18 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 91.6 0.135 23521 21546 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 82 0.3 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1T4F 2.3 19.86 3 21546 20724 1121 99.74 0.25065 0.24743 0.2451 0.3102 0.3089 RANDOM 26.253
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] -0.41 -0.01 -0.23 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.475 r_dihedral_angle_4_deg 31.971 r_dihedral_angle_3_deg 18.608 r_dihedral_angle_1_deg 8.761 r_scangle_it 2.192 r_angle_refined_deg 1.426 r_scbond_it 1.354 r_mcangle_it 1.047 r_mcbond_it 0.601 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.475 r_dihedral_angle_4_deg 31.971 r_dihedral_angle_3_deg 18.608 r_dihedral_angle_1_deg 8.761 r_scangle_it 2.192 r_angle_refined_deg 1.426 r_scbond_it 1.354 r_mcangle_it 1.047 r_mcbond_it 0.601 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.232 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.138 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2377 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XSCALE data scaling MOLREP phasing