6LCN

Crystal structure of Serine Acetyltransferase from Planctomyces limnophilus at 2.15A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	278	0.1M MES pH=6.5, 12% w/v PEG 20,000

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.719	α = 90
b = 113.165	β = 90
c = 230.133	γ = 90

Symmetry
Space Group	P 21 21 21

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		2017-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5417

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.15	47.596	99.64	0.09531	0.1078	0.04956	0.997	14.44	4.7		120745			32.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.227	99.23		0.742	0.8414	0.3909	0.658		4.5

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	3F1X	2.15	47.596	120491	1990	99.694	0.187	0.1866	0.223	38.87

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]
1.514			0.095		-1.609

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.367
r_dihedral_angle_4_deg	18.619
r_dihedral_angle_3_deg	14.521
r_lrange_it	9.109
r_dihedral_angle_1_deg	6.52
r_scangle_it	6.248
r_mcangle_it	4.636
r_scbond_it	4.391
r_mcbond_it	3.148
r_angle_refined_deg	1.475

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.367
r_dihedral_angle_4_deg	18.619
r_dihedral_angle_3_deg	14.521
r_lrange_it	9.109
r_dihedral_angle_1_deg	6.52
r_scangle_it	6.248
r_mcangle_it	4.636
r_scbond_it	4.391
r_mcbond_it	3.148
r_angle_refined_deg	1.475
r_nbtor_refined	0.309
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.209
r_symmetry_xyhbond_nbd_refined	0.15
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.107
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14076
Nucleic Acid Atoms
Solvent Atoms	766
Heterogen Atoms	67

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.