8H1Q

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-serine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG4000, sodium acetate, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.2645.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.282α = 90
b = 61.282β = 90
c = 207.788γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

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
11.55099.80.998159.364186
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)
11.51.590.949

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-VALUE3A2B1.545.9464160659199.20.1510.1480.18419.881
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]
0.260.26-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.087
r_dihedral_angle_4_deg16.641
r_dihedral_angle_3_deg14.265
r_dihedral_angle_1_deg6.238
r_lrange_it5.281
r_lrange_other5.024
r_scangle_it3.859
r_scangle_other3.859
r_scbond_it2.579
r_scbond_other2.579
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.087
r_dihedral_angle_4_deg16.641
r_dihedral_angle_3_deg14.265
r_dihedral_angle_1_deg6.238
r_lrange_it5.281
r_lrange_other5.024
r_scangle_it3.859
r_scangle_other3.859
r_scbond_it2.579
r_scbond_other2.579
r_mcangle_it2.009
r_mcangle_other2.009
r_angle_refined_deg1.829
r_angle_other_deg1.572
r_mcbond_it1.473
r_mcbond_other1.473
r_chiral_restr_other0.257
r_nbd_refined0.222
r_symmetry_nbd_other0.179
r_xyhbond_nbd_refined0.176
r_nbd_other0.176
r_symmetry_xyhbond_nbd_refined0.175
r_nbtor_refined0.171
r_symmetry_nbd_refined0.137
r_chiral_restr0.097
r_symmetry_nbtor_other0.082
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_xyhbond_nbd_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3035
Nucleic Acid Atoms
Solvent Atoms502
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing