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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 25% PEG3350, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.15 42.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.73 α = 90 b = 58.87 β = 92 c = 96.11 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 mirrors 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 1.9 40 96 0.055 32474 31292 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) 1.9 2 86 0.195 7
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 1.9 19.78 2 30432 1626 98.82 0.19978 0.19657 0.1987 0.2571 0.2638 RANDOM 17.327
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] 0.99 -0.49 0.04 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.988 r_dihedral_angle_4_deg 18.242 r_dihedral_angle_3_deg 14.745 r_dihedral_angle_1_deg 10.365 r_scangle_it 2.722 r_scbond_it 1.861 r_angle_refined_deg 1.354 r_mcangle_it 1.261 r_angle_other_deg 1.089 r_mcbond_it 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.988 r_dihedral_angle_4_deg 18.242 r_dihedral_angle_3_deg 14.745 r_dihedral_angle_1_deg 10.365 r_scangle_it 2.722 r_scbond_it 1.861 r_angle_refined_deg 1.354 r_mcangle_it 1.261 r_angle_other_deg 1.089 r_mcbond_it 0.85 r_symmetry_vdw_refined 0.351 r_symmetry_vdw_other 0.269 r_nbd_refined 0.207 r_nbd_other 0.184 r_symmetry_hbond_refined 0.183 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.163 r_mcbond_other 0.161 r_chiral_restr 0.127 r_nbtor_other 0.085 r_bond_refined_d 0.01 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 3151 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling MOLREP phasing