8H21

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-alanine

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
2.23	44.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.234	α = 90
b = 61.234	β = 90
c = 208.182	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		2021-04-14	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	1.54	50	98.3	0.999	27.1	17.8		58899

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	1.54	1.63			0.965

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	1.54	45.956	58868	5972	98.39	0.177	0.1722	0.2164	16.383

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]
0.012			0.012		-0.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.483
r_dihedral_angle_4_deg	17.791
r_dihedral_angle_3_deg	14.109
r_dihedral_angle_1_deg	6.492
r_lrange_it	4.993
r_lrange_other	4.992
r_scangle_it	3.314
r_scangle_other	3.313
r_scbond_it	2.155
r_scbond_other	2.155
r_mcangle_other	1.828
r_mcangle_it	1.827
r_angle_refined_deg	1.769
r_angle_other_deg	1.524
r_mcbond_it	1.266
r_mcbond_other	1.264
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.19
r_nbd_other	0.178
r_symmetry_nbd_other	0.176
r_symmetry_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.169
r_symmetry_nbd_refined	0.147
r_symmetry_xyhbond_nbd_other	0.095
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.012
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	3035
Nucleic Acid Atoms
Solvent Atoms	493
Heterogen Atoms	45

Software

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