8H20

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Glycine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG4000, sodium acetate, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.2545.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.573α = 90
b = 61.573β = 90
c = 207.774γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-20MSINGLE 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
11.45501000.99922.89.672011
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)
11.451.540.969

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-VALUE3A2B1.4546.05972008729199.9780.1920.18820.228920.116
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]
0.6950.695-1.389
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.003
r_dihedral_angle_3_deg14.407
r_dihedral_angle_4_deg12.998
r_dihedral_angle_1_deg6.451
r_lrange_it5.249
r_lrange_other5.248
r_scangle_it4.141
r_scangle_other4.14
r_scbond_it2.734
r_scbond_other2.733
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.003
r_dihedral_angle_3_deg14.407
r_dihedral_angle_4_deg12.998
r_dihedral_angle_1_deg6.451
r_lrange_it5.249
r_lrange_other5.248
r_scangle_it4.141
r_scangle_other4.14
r_scbond_it2.734
r_scbond_other2.733
r_mcangle_it2.176
r_mcangle_other2.176
r_angle_refined_deg1.894
r_mcbond_it1.652
r_mcbond_other1.652
r_angle_other_deg1.532
r_nbd_refined0.228
r_symmetry_xyhbond_nbd_refined0.208
r_symmetry_nbd_other0.18
r_nbd_other0.172
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.167
r_symmetry_nbd_refined0.117
r_chiral_restr0.099
r_symmetry_nbtor_other0.082
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3035
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing