8H1W

Serine Palmitoyltransferase from Sphingobacterium multivorum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP297PEG4000, sodium acetate, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.2445.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.612α = 90
b = 61.612β = 90
c = 208.349γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225-HS2018-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B20.9SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.450100120.610.880227
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.480.848

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3A2B1.443.60480166817999.9730.1720.16850.201721.099
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]
0.4680.468-0.936
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.929
r_dihedral_angle_3_deg14.371
r_dihedral_angle_4_deg11.422
r_dihedral_angle_1_deg6.567
r_lrange_it5.484
r_lrange_other5.484
r_scangle_it3.872
r_scangle_other3.871
r_scbond_it2.736
r_scbond_other2.736
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.929
r_dihedral_angle_3_deg14.371
r_dihedral_angle_4_deg11.422
r_dihedral_angle_1_deg6.567
r_lrange_it5.484
r_lrange_other5.484
r_scangle_it3.872
r_scangle_other3.871
r_scbond_it2.736
r_scbond_other2.736
r_mcangle_it2.084
r_mcangle_other2.084
r_angle_refined_deg1.895
r_angle_other_deg1.564
r_mcbond_it1.548
r_mcbond_other1.547
r_nbd_refined0.228
r_symmetry_nbd_refined0.196
r_xyhbond_nbd_refined0.195
r_symmetry_nbd_other0.181
r_symmetry_xyhbond_nbd_refined0.176
r_nbtor_refined0.171
r_nbd_other0.168
r_symmetry_xyhbond_nbd_other0.112
r_chiral_restr0.096
r_symmetry_nbtor_other0.083
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3050
Nucleic Acid Atoms
Solvent Atoms534
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing