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Structure of human MDMX protein in complex with a small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 300 0.2M Na/K-tartrate, 0.1M Tri-sodium-citrate, 2M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.15 42.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.97 α = 90 b = 80.97 β = 90 c = 80.97 γ = 90
Symmetry Space Group I 21 3
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 165 mm monochromator, mirror 2009-07-17 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) R Sym 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 1.5 30 84.5 0.042 0.072 22.55 11 14279 12097 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) 1.5 1.6 62.7 0.152 6.39 9 1556
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DAB 1.5 20 2 12097 11482 609 84.55 0.176 0.174 0.206 0.2123 RANDOM 13.554
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 46.357 r_dihedral_angle_4_deg 15.548 r_dihedral_angle_3_deg 15.306 r_dihedral_angle_1_deg 7.103 r_angle_other_deg 4.523 r_scangle_it 4.089 r_sphericity_free 3.505 r_scbond_it 2.717 r_angle_refined_deg 2.455 r_mcangle_it 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.357 r_dihedral_angle_4_deg 15.548 r_dihedral_angle_3_deg 15.306 r_dihedral_angle_1_deg 7.103 r_angle_other_deg 4.523 r_scangle_it 4.089 r_sphericity_free 3.505 r_scbond_it 2.717 r_angle_refined_deg 2.455 r_mcangle_it 1.81 r_rigid_bond_restr 1.616 r_sphericity_bonded 1.401 r_mcbond_it 0.985 r_mcbond_other 0.608 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 658 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 93
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling