4WH9

Structure of the CDC25B Phosphatase Catalytic Domain with Bound Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A2K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298(NH4)2SO4, Tris, TCEP
Crystal Properties
Matthews coefficientSolvent content
3.1861.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.66α = 90
b = 71.47β = 90
c = 73.94γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.3351.391000.09810.53.663905
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)
11.331.41000.461.33.5

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 REPLACEMENTTHROUGHOUT2A2K1.551.3942329222699.980.12730.1260.15201RANDOM19.655
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]
-0.020.03-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.937
r_dihedral_angle_4_deg22.274
r_sphericity_bonded19.02
r_dihedral_angle_3_deg12.318
r_rigid_bond_restr8.932
r_dihedral_angle_1_deg6.891
r_scangle_other6.783
r_scbond_it6.465
r_scbond_other6.465
r_long_range_B_refined6.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.937
r_dihedral_angle_4_deg22.274
r_sphericity_bonded19.02
r_dihedral_angle_3_deg12.318
r_rigid_bond_restr8.932
r_dihedral_angle_1_deg6.891
r_scangle_other6.783
r_scbond_it6.465
r_scbond_other6.465
r_long_range_B_refined6.167
r_long_range_B_other5.433
r_mcangle_it3.407
r_mcangle_other3.405
r_mcbond_other3.033
r_mcbond_it3.031
r_angle_refined_deg1.928
r_angle_other_deg1.422
r_chiral_restr0.13
r_gen_planes_refined0.015
r_bond_refined_d0.012
r_gen_planes_other0.01
r_bond_other_d0.001
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_scangle_it
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1472
Nucleic Acid Atoms
Solvent Atoms296
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing