4CZ5

Truncated tetramerization domain of zebrafish p53 (crystal form I)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9293SITTING DROP VAPOR DIFFUSION AT 20 DEGREE C; PROTEIN SOLUTION: 17 MG/ML IN 20 MM TRIS PH 7.5, 50 MM NACL, 5 MM DTT; CRYSTALLIZATION BUFFER: 2.4 M AMMONIUM SULFATE, 100 MM BICINE, PH 9.0
Crystal Properties
Matthews coefficientSolvent content
1.935

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.232α = 90
b = 33.685β = 90
c = 101.805γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.0228.0999.80.0319.35.2590762
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)
11.021.0899.90.5435

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.0228.156018298299.710.158660.157590.17846RANDOM15.458
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]
-0.422.14-1.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.623
r_sphericity_free27.875
r_dihedral_angle_3_deg11.787
r_dihedral_angle_4_deg10.555
r_sphericity_bonded9.268
r_dihedral_angle_1_deg4.201
r_scbond_it2.243
r_rigid_bond_restr2.195
r_mcangle_it1.559
r_angle_refined_deg1.339
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.623
r_sphericity_free27.875
r_dihedral_angle_3_deg11.787
r_dihedral_angle_4_deg10.555
r_sphericity_bonded9.268
r_dihedral_angle_1_deg4.201
r_scbond_it2.243
r_rigid_bond_restr2.195
r_mcangle_it1.559
r_angle_refined_deg1.339
r_mcbond_it1.224
r_mcbond_other1.222
r_angle_other_deg0.721
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms986
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement