9U39 | pdb_00009u39

Crystal structure of Serine Acetyltransferase (SAT) from Planctomyces limnophilus in complex with its substrate serine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LCN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	278	35% v/v 2-methyl-2,4-pentanediol, 100mM HEPES pH 7.5, 200mm NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.98	α = 90
b = 90.03	β = 114.796
c = 122.544	γ = 90

Symmetry
Space Group	I 1 2 1

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		2020-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54179

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	2.218	40.858	93.25	0.06473	0.07397	0.03511	0.999	11.94	4.2		47993

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.26	78.57		0.434	0.5074	0.847		3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.218	40.858	47974	2329	93.273	0.216	0.2131	0.2156	0.2692	0.2735	58.739

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]
1.049		3.02	-0.723		-2.184

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.034
r_lrange_it	14.799
r_dihedral_angle_6_deg	14.261
r_scangle_it	11.316
r_mcangle_it	9.556
r_dihedral_angle_2_deg	8.976
r_scbond_it	7.955
r_dihedral_angle_1_deg	6.726
r_mcbond_it	6.68
r_angle_refined_deg	1.892
r_nbtor_refined	0.309
r_symmetry_nbd_refined	0.234
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.136
r_ncsr_local_group_3	0.082
r_ncsr_local_group_1	0.078
r_symmetry_xyhbond_nbd_refined	0.077
r_ncsr_local_group_2	0.072
r_bond_refined_d	0.008
r_metal_ion_refined	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6936
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing