3LBJ

Structure of human MDMX protein in complex with a small molecule inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.63000.2M Na/K-tartrate, 0.1M Tri-sodium-citrate, 2M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.1542.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.97α = 90
b = 80.97β = 90
c = 80.97γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMAR CCD 165 mmmonochromator, mirror2009-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00SLSX10SA

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.53084.50.0420.07222.5511142791209722
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)
1.51.662.70.1526.3991556

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT3DAB1.5202120971148260984.550.1760.1740.206RANDOM13.554
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.357
r_dihedral_angle_4_deg15.548
r_dihedral_angle_3_deg15.306
r_dihedral_angle_1_deg7.103
r_angle_other_deg4.523
r_scangle_it4.089
r_sphericity_free3.505
r_scbond_it2.717
r_angle_refined_deg2.455
r_mcangle_it1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.357
r_dihedral_angle_4_deg15.548
r_dihedral_angle_3_deg15.306
r_dihedral_angle_1_deg7.103
r_angle_other_deg4.523
r_scangle_it4.089
r_sphericity_free3.505
r_scbond_it2.717
r_angle_refined_deg2.455
r_mcangle_it1.81
r_rigid_bond_restr1.616
r_sphericity_bonded1.401
r_mcbond_it0.985
r_mcbond_other0.608
r_chiral_restr0.104
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_gen_planes_other0.006
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 AtomsNumber
Protein Atoms658
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms93

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling