5X0E

Free serine kinase (E30A mutant) in complex with phosphoserine and AMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VK1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.9293PEG 3350, serine
Crystal Properties
Matthews coefficientSolvent content
2.1943.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.667α = 90
b = 43.224β = 90
c = 157.519γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2015-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.100Photon FactoryBL-1A

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
125095.924.35.216587

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 REPLACEMENTTHROUGHOUT1VK12501568086595.950.182980.180860.22188RANDOM15.264
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]
-0.461.64-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.306
r_dihedral_angle_3_deg12.136
r_dihedral_angle_4_deg9.491
r_dihedral_angle_1_deg6.501
r_long_range_B_refined2.634
r_long_range_B_other2.474
r_scangle_other1.584
r_angle_refined_deg1.396
r_mcangle_it1.122
r_mcangle_other1.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.306
r_dihedral_angle_3_deg12.136
r_dihedral_angle_4_deg9.491
r_dihedral_angle_1_deg6.501
r_long_range_B_refined2.634
r_long_range_B_other2.474
r_scangle_other1.584
r_angle_refined_deg1.396
r_mcangle_it1.122
r_mcangle_other1.122
r_scbond_other0.966
r_scbond_it0.964
r_angle_other_deg0.87
r_mcbond_it0.677
r_mcbond_other0.677
r_chiral_restr0.078
r_bond_refined_d0.009
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 Atoms1911
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing