3FE7

Crystal Structure of HdmX bound to the p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-Trp-Glu-Ac3c-Leu-NH2 at 1.35A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GV2PDB ENTRY 2GV2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62773.1M AmSo4, 1% MPD, 4% polypropyleneglycol, 0.1M MES, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4950.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.294α = 90
b = 43.294β = 90
c = 65.59γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99975SLSX10SA

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
11.352094.90.05732.8526.925341
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)
1.351.461.30.2661.61647

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2GV21.352025273127895.160.1920.1920.209RANDOM16.964
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]
-0.11-0.110.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.738
r_dihedral_angle_4_deg19.477
r_dihedral_angle_3_deg11.012
r_dihedral_angle_1_deg6.018
r_scangle_it3.954
r_scbond_it2.527
r_mcangle_it1.587
r_angle_refined_deg1.212
r_mcbond_it1.01
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.738
r_dihedral_angle_4_deg19.477
r_dihedral_angle_3_deg11.012
r_dihedral_angle_1_deg6.018
r_scangle_it3.954
r_scbond_it2.527
r_mcangle_it1.587
r_angle_refined_deg1.212
r_mcbond_it1.01
r_nbtor_refined0.308
r_symmetry_hbond_refined0.203
r_symmetry_vdw_refined0.201
r_nbd_refined0.195
r_xyhbond_nbd_refined0.1
r_chiral_restr0.089
r_bond_refined_d0.009
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms752
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction