3CR7

Crystal structure of N-terminal truncation of APS Kinase from Penicillium chrysogenum: Ternary structure with ADP and PAPS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M7Gpoly alanine model of pdb entry 1M7G A chain

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293bis tris, PEG 3350, ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.58α = 90
b = 82.594β = 90
c = 139.009γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Double-crystal monochromator2007-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL1-50.9194SSRLBL1-5

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.531.71899.60.0840.0847.53.63158231427-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.561000.4860.4861.53.62290

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTpoly alanine model of pdb entry 1M7G A chain2.531.7150.0131427227892.880.2020.2010.1980.279random37.49
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]
-5.379-2.8237.393
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d22.26
f_angle_d1.421
f_chiral_restr0.073
f_bond_d0.01
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5562
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms173

Software

Software
Software NamePurpose
SCALAdata scaling
EPMRphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction