4IJ5

Crystal Structure of a Novel-type Phosphoserine Phosphatase from <i>Hydrogenobacter thermophilus</i> TK-6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293100mM HEPES-NaOH, 10%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3246.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.81α = 90
b = 73.63β = 90
c = 124.28γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR225HE2011-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.0000SPring-8BL32XU

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
11.536.18.67368473612

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 REPLACEMENTTHROUGHOUT1H2E1.536.173608371499.880.18430.18360.1966RANDOM16.45
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]
0.22-0.06-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.824
r_dihedral_angle_4_deg15.717
r_dihedral_angle_3_deg11.974
r_dihedral_angle_1_deg5.932
r_angle_refined_deg1.272
r_angle_other_deg0.772
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.824
r_dihedral_angle_4_deg15.717
r_dihedral_angle_3_deg11.974
r_dihedral_angle_1_deg5.932
r_angle_refined_deg1.272
r_angle_other_deg0.772
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3456
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling