6Q9Y

HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 16 AT 1.20A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q9Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62982.5M AmSO4, 0.1M KSCN, 1% v/v MPD, 0.1M MES
Crystal Properties
Matthews coefficientSolvent content
2.0539.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.492α = 90
b = 42.426β = 90
c = 107.421γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99999SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.219.7399.90.0350.039125.76.26013116.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2399.20.5170.5710.8713.45.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6Q9Q1.219.7357124300799.890.1620.16080.1842RANDOM14.678
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]
0.010.04-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.079
r_dihedral_angle_4_deg11.53
r_dihedral_angle_3_deg11.023
r_dihedral_angle_1_deg5.876
r_sphericity_free4.242
r_sphericity_bonded3.546
r_rigid_bond_restr1.436
r_angle_refined_deg1.268
r_chiral_restr0.095
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.079
r_dihedral_angle_4_deg11.53
r_dihedral_angle_3_deg11.023
r_dihedral_angle_1_deg5.876
r_sphericity_free4.242
r_sphericity_bonded3.546
r_rigid_bond_restr1.436
r_angle_refined_deg1.268
r_chiral_restr0.095
r_bond_refined_d0.009
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1381
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms52

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction