8GUH

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Tris

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A2B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	PEG4000, sodium acetate, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.321	α = 90
b = 61.321	β = 90
c = 208.573	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		2019-09-09	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)	Rrim I (All)	Rpim I (All)	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	1.65	50	96.8	0.063	0.024	0.999	23.4	8.9		47616

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.75			0.222	0.128	0.956	6.4

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	1.65	46.031	47601	4916	96.957	0.174	0.1695	0.2143	15.038

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]
-0.344			-0.344		0.687

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.688
r_dihedral_angle_4_deg	15.241
r_dihedral_angle_3_deg	14.164
r_dihedral_angle_1_deg	6.575
r_lrange_it	4.588
r_lrange_other	4.587
r_scangle_it	2.899
r_scangle_other	2.898
r_scbond_it	1.916
r_scbond_other	1.916
r_angle_refined_deg	1.675
r_mcangle_it	1.662
r_mcangle_other	1.662
r_angle_other_deg	1.47
r_mcbond_it	1.125
r_mcbond_other	1.122
r_nbd_refined	0.218
r_nbd_other	0.194
r_xyhbond_nbd_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.185
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.165
r_symmetry_nbd_refined	0.161
r_symmetry_xyhbond_nbd_other	0.137
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.08
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	456
Heterogen Atoms	47

Software

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