8IYP

Crystal structure of serine palmitoyltransferase soaked in 190 mM D-serine solution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A2B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG4000, sodium acetate, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.244.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.975α = 90
b = 60.975β = 90
c = 207.311γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2017-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.9SPring-8BL38B1

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
11.655099.2138.712.947801
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)
11.651.750.991

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-VALUE3A2B1.65142.24847801494699.150.1520.14870.184217.502
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]
0.6180.618-1.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.874
r_dihedral_angle_3_deg14.889
r_dihedral_angle_1_deg6.322
r_dihedral_angle_2_deg6.237
r_lrange_it5.286
r_lrange_other5.286
r_scangle_it4.003
r_scangle_other4.002
r_scbond_it2.687
r_scbond_other2.686
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.874
r_dihedral_angle_3_deg14.889
r_dihedral_angle_1_deg6.322
r_dihedral_angle_2_deg6.237
r_lrange_it5.286
r_lrange_other5.286
r_scangle_it4.003
r_scangle_other4.002
r_scbond_it2.687
r_scbond_other2.686
r_mcangle_it2.117
r_mcangle_other2.117
r_angle_refined_deg1.682
r_mcbond_it1.597
r_mcbond_other1.597
r_angle_other_deg0.569
r_nbd_refined0.233
r_chiral_restr_other0.222
r_symmetry_nbd_other0.189
r_nbtor_refined0.181
r_symmetry_xyhbond_nbd_refined0.163
r_nbd_other0.162
r_xyhbond_nbd_refined0.161
r_symmetry_nbd_refined0.131
r_chiral_restr0.083
r_symmetry_nbtor_other0.079
r_symmetry_xyhbond_nbd_other0.016
r_xyhbond_nbd_other0.011
r_bond_refined_d0.01
r_gen_planes_refined0.009
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 Atoms407
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing