4IJ6

Crystal Structure of a Novel-type Phosphoserine Phosphatase Mutant (H9A) from <i>Hydrogenobacter thermophilus</i> TK-6 in Complex with L-phosphoserine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IJ5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6293100 mM sodium acetate trihydrate, 20 mM calcium chloride dihydrate, and 30% (v/v)-2-methyl-2,4-pentanediol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1442.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.33α = 90
b = 68.92β = 90
c = 123.55γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702012-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0000Photon FactoryAR-NE3A

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
11.838.23985739566

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 REPLACEMENTTHROUGHOUT4IJ51.838.1539565198999.370.19180.19040.2175RANDOM17.555
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]
0.370.43-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.674
r_dihedral_angle_4_deg13.424
r_dihedral_angle_3_deg11.42
r_dihedral_angle_1_deg5.77
r_angle_refined_deg1.099
r_angle_other_deg0.682
r_chiral_restr0.061
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.674
r_dihedral_angle_4_deg13.424
r_dihedral_angle_3_deg11.42
r_dihedral_angle_1_deg5.77
r_angle_refined_deg1.099
r_angle_other_deg0.682
r_chiral_restr0.061
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3347
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling