8H1Y

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-homoserine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	PEG4000, sodium acetate, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.238	α = 90
b = 61.238	β = 90
c = 208.097	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	IMAGE PLATE	RIGAKU RAXIS VII		2020-12-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-X	1.5418

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	1.55	50	98.3	0.997	13.6	8.3		57736

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	1.55	1.64			0.924

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	1.55	45.95	57730	5954	98.363	0.187	0.1826	0.2233	13.975

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]
-0.342			-0.342		0.684

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.719
r_dihedral_angle_4_deg	14.44
r_dihedral_angle_3_deg	14.37
r_dihedral_angle_1_deg	6.613
r_lrange_it	4.232
r_lrange_other	3.936
r_scangle_it	2.654
r_scangle_other	2.654
r_scbond_it	1.739
r_scbond_other	1.739
r_angle_refined_deg	1.698
r_mcangle_it	1.546
r_mcangle_other	1.546
r_angle_other_deg	1.482
r_mcbond_it	1.064
r_mcbond_other	1.064
r_nbd_refined	0.219
r_nbd_other	0.181
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.167
r_symmetry_nbd_refined	0.164
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3035
Nucleic Acid Atoms
Solvent Atoms	475
Heterogen Atoms	43

Software

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