5X0J

Free serine kinase (E30Q mutant) in complex with phosphoserine and AMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5X0E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.7293PEG 3350, serine
Crystal Properties
Matthews coefficientSolvent content
2.2144.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.824α = 90
b = 43.4β = 90
c = 157.545γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 315r2016-02-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

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
11.435097.521.76.245510

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5X0E1.435043174227597.430.181340.180450.19827RANDOM16.253
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]
-0.450.350.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.238
r_dihedral_angle_3_deg11.259
r_dihedral_angle_4_deg10.86
r_dihedral_angle_1_deg6.097
r_long_range_B_refined3.287
r_long_range_B_other3.051
r_angle_refined_deg1.369
r_angle_other_deg0.861
r_scangle_other0.827
r_mcangle_it0.655
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.238
r_dihedral_angle_3_deg11.259
r_dihedral_angle_4_deg10.86
r_dihedral_angle_1_deg6.097
r_long_range_B_refined3.287
r_long_range_B_other3.051
r_angle_refined_deg1.369
r_angle_other_deg0.861
r_scangle_other0.827
r_mcangle_it0.655
r_mcangle_other0.654
r_scbond_other0.509
r_scbond_it0.508
r_mcbond_it0.377
r_mcbond_other0.377
r_chiral_restr0.081
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1906
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
REFMACphasing