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Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YCR PDB ENTRY 1YCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 300 30% PEG300, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 1.99 38.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.43 α = 90 b = 30.81 β = 107.43 c = 70.09 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 100 CCD MARRESEARCH mirror 2008-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 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 1.8 30 94.5 0.069 15.9 26003 24703 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) 1.8 2 85.1 0.223 6.9
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 THROUGHOUT PDB ENTRY 1YCR 1.8 24.49 2 23573 1271 96.92 0.2071 0.20512 0.2076 0.24292 0.2475 RANDOM 14.882
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] -0.09 -0.09 0.06 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.842 r_dihedral_angle_4_deg 22.751 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 5.885 r_scangle_it 2.575 r_scbond_it 1.737 r_mcangle_it 1.352 r_angle_refined_deg 1.236 r_angle_other_deg 0.88 r_mcbond_it 0.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.842 r_dihedral_angle_4_deg 22.751 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 5.885 r_scangle_it 2.575 r_scbond_it 1.737 r_mcangle_it 1.352 r_angle_refined_deg 1.236 r_angle_other_deg 0.88 r_mcbond_it 0.863 r_symmetry_vdw_other 0.299 r_nbd_refined 0.211 r_nbd_other 0.185 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.15 r_mcbond_other 0.143 r_symmetry_hbond_refined 0.141 r_nbtor_other 0.088 r_chiral_restr 0.073 r_symmetry_vdw_refined 0.05 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1532 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling MOLREP phasing