8H29

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-threonine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG4000, sodium acetate, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.083	α = 90
b = 61.083	β = 90
c = 207.89	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2020-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	0.98	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.45	50	99.9	1	31.4	9.3		70978

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.54			0.967

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3A2B	1.45	43.23	70922	7165	99.924	0.148	0.1446	0.174	17.457

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]
-0.003			-0.003		0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.535
r_dihedral_angle_4_deg	16.645
r_dihedral_angle_3_deg	13.562
r_dihedral_angle_1_deg	6.425
r_lrange_it	5.059
r_lrange_other	5.058
r_scangle_it	3.461
r_scangle_other	3.461
r_scbond_it	2.47
r_scbond_other	2.469
r_angle_refined_deg	1.867
r_mcangle_it	1.786
r_mcangle_other	1.786
r_angle_other_deg	1.585
r_mcbond_it	1.318
r_mcbond_other	1.318
r_nbd_refined	0.229
r_nbd_other	0.192
r_xyhbond_nbd_refined	0.185
r_symmetry_nbd_other	0.18
r_symmetry_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.159
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3027
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing