4CZ7

Truncated tetramerization domain of zebrafish p53 (crystal form III)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5293SITTING 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: 1.8 M SODIUM/POTASSIUM PHOSPHATE, PH 5.0.
Crystal Properties
Matthews coefficientSolvent content
238

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.734α = 90
b = 45.717β = 92.6
c = 55.486γ = 90
Symmetry
Space GroupC 1 2 1

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
11.127.794.80.0612.13.5688312
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)
11.11.1687.40.176.53.3

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 REPLACEMENTTHROUGHOUT1.127.765375345694.490.144150.142980.16588RANDOM12.823
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]
-0.040.640.39-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.902
r_sphericity_free27.047
r_dihedral_angle_4_deg15.48
r_dihedral_angle_3_deg10.431
r_sphericity_bonded7.656
r_dihedral_angle_1_deg4.761
r_scbond_it1.604
r_rigid_bond_restr1.48
r_mcangle_it1.35
r_angle_refined_deg1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.902
r_sphericity_free27.047
r_dihedral_angle_4_deg15.48
r_dihedral_angle_3_deg10.431
r_sphericity_bonded7.656
r_dihedral_angle_1_deg4.761
r_scbond_it1.604
r_rigid_bond_restr1.48
r_mcangle_it1.35
r_angle_refined_deg1.24
r_mcbond_it0.972
r_mcbond_other0.969
r_angle_other_deg0.689
r_chiral_restr0.075
r_bond_refined_d0.008
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 Atoms1541
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement