3W69

Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.12932.4M Ammonium sulfate, 5% PEG 200, 0.1M Tris HCl, pH 8.1 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.5164.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.562α = 90
b = 65.761β = 90
c = 81.436γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VIIconfocal mirrors2007-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.944.895.50.0698.32.12242722162
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9295.20.4751.522930

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1RV11.921.18221622096910791000.210380.208940.2381RANDOM30.626
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]
1.230.19-1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.59
r_dihedral_angle_4_deg25.888
r_dihedral_angle_3_deg17.486
r_dihedral_angle_1_deg5.582
r_scangle_it3.292
r_angle_refined_deg2.127
r_scbond_it2.076
r_mcangle_it1.555
r_mcbond_it0.867
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.59
r_dihedral_angle_4_deg25.888
r_dihedral_angle_3_deg17.486
r_dihedral_angle_1_deg5.582
r_scangle_it3.292
r_angle_refined_deg2.127
r_scbond_it2.076
r_mcangle_it1.555
r_mcbond_it0.867
r_nbtor_refined0.317
r_nbd_refined0.219
r_symmetry_hbond_refined0.197
r_symmetry_vdw_refined0.196
r_xyhbond_nbd_refined0.155
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 AtomsNumber
Protein Atoms1414
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms109

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
PROCESSdata reduction
SCALAdata scaling