1YMD

Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfonic form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QB0PDB ENTRY 1QB0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.25DTT, Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K
Crystal Properties
Matthews coefficientSolvent content
2.9257.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.702α = 90
b = 71.152β = 90
c = 74.431γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.735.74288522885218.1

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 1QB01.735.7428852288522865970.190.190.1880.209RANDOM20.4
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]
3.04-1.69-1.36
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.7
c_scangle_it3.4
c_scbond_it2.21
c_mcangle_it1.81
c_improper_angle_d1.68
c_angle_deg1.5
c_mcbond_it1.15
c_bond_d0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1430
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms1

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing