9M7A | pdb_00009m7a

Crystal structure of Serine Acetyltransferase (SAT) from Planctomyces limnophilus in complex with its inhibitor (Cysteine)

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	6.5	278	0.02 M Magnesium chloride hexahydrate, 0.05 M PIPES pH7.5, 10% w/v 1,6-hexanediol, 0.001 M spermine

Crystal Properties
Matthews coefficient	Solvent content
2.5	51.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.749	α = 90
b = 88.8	β = 113.22
c = 101.4	γ = 90

Symmetry
Space Group	C 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	MAR scanner 345 mm plate		2021-01-20	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.45	46.59	93.55	0.04985	0.995	10.26	2		36602			35.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.538	100		0.2263	0.907		2

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	2.45	46.59	36049	1709	93.777	0.241	0.2394	0.2393	0.2837	0.2838	35.37

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]
4.268		-3.304	-0.1		-0.974

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.223
r_dihedral_angle_4_deg	19.037
r_dihedral_angle_3_deg	17.651
r_lrange_it	9.619
r_dihedral_angle_1_deg	7.17
r_scangle_it	6.428
r_mcangle_it	5.536
r_scbond_it	4.085
r_mcbond_it	3.412
r_angle_refined_deg	1.544
r_nbtor_refined	0.311
r_symmetry_nbd_refined	0.258
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.11
r_symmetry_xyhbond_nbd_refined	0.073
r_ncsr_local_group_3	0.067
r_ncsr_local_group_2	0.052
r_ncsr_local_group_1	0.051
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6925
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	14

Software

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