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Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.1 293 2.4M Ammonium sulfate, 5% PEG 200, 0.1M Tris HCl, pH 8.1 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.51 64.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.562 α = 90 b = 65.761 β = 90 c = 81.436 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII confocal mirrors 2007-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 44.8 95.5 0.069 8.3 2.1 22427 22162
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 1.9 2 95.2 0.475 1.5 2 2930
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1RV1 1.9 21.18 22162 20969 1079 100 0.21038 0.20894 0.21 0.2381 0.2401 RANDOM 30.626
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] 1.23 0.19 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.59 r_dihedral_angle_4_deg 25.888 r_dihedral_angle_3_deg 17.486 r_dihedral_angle_1_deg 5.582 r_scangle_it 3.292 r_angle_refined_deg 2.127 r_scbond_it 2.076 r_mcangle_it 1.555 r_mcbond_it 0.867 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.59 r_dihedral_angle_4_deg 25.888 r_dihedral_angle_3_deg 17.486 r_dihedral_angle_1_deg 5.582 r_scangle_it 3.292 r_angle_refined_deg 2.127 r_scbond_it 2.076 r_mcangle_it 1.555 r_mcbond_it 0.867 r_nbtor_refined 0.317 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.197 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1414 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 109
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement PROCESS data reduction SCALA data scaling