3D09

Human p53 core domain with hot spot mutation R249S and second-site suppressor mutations H168R and T123A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.12930.2M Sodium Acetate, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.518α = 90
b = 45.518β = 90
c = 327.424γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Sagitally focusing Ge(220) and a multilayer2007-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.93400ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.94498.80.06933.59.9170681706823.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9390.40.2924.55.4729

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1TSR1.937.09160721607285998.80.20680.206780.203870.26209RANDOM23.366
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]
-0.01-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.39
r_dihedral_angle_3_deg12.769
r_dihedral_angle_4_deg11.764
r_scangle_it8.326
r_scbond_it6.761
r_dihedral_angle_1_deg6.389
r_mcangle_it5.081
r_mcbond_it3.844
r_angle_refined_deg1.422
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.39
r_dihedral_angle_3_deg12.769
r_dihedral_angle_4_deg11.764
r_scangle_it8.326
r_scbond_it6.761
r_dihedral_angle_1_deg6.389
r_mcangle_it5.081
r_mcbond_it3.844
r_angle_refined_deg1.422
r_nbtor_refined0.304
r_symmetry_vdw_refined0.23
r_symmetry_hbond_refined0.207
r_xyhbond_nbd_refined0.202
r_nbd_refined0.2
r_metal_ion_refined0.129
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_metal_ion_other
r_nbd_other
r_symmetry_vdw_other
r_angle_other_deg
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbtor_other
r_mcbond_other
r_gen_planes_other
r_bond_other_d
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1517
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing