9R0W | pdb_00009r0w

Crystal structure of glutathione transferase iota 1 from Synechocystis sp. PCC 6803 in complex with FMN

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		277	30% PEG 4000, 200 mM LiSO4, 100 mM Tris

Crystal Properties
Matthews coefficient	Solvent content
3.71	66.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.313	α = 90
b = 173.927	β = 90
c = 318.382	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS EIGER X 9M		2019-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.98011	SOLEIL	PROXIMA 2

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	2.71	48.791	99.2	1	22.3	14		92848

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	2.71	2.78			0.83	1.6

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	2.71	48.791	92753	4658	99.796	0.21	0.2084	0.2084	0.2417	0.2418	76.239

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]
2.031			2.758		-4.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.947
r_lrange_it	16.222
r_dihedral_angle_6_deg	15.327
r_scangle_it	13.836
r_mcangle_it	12.948
r_scbond_it	10.211
r_mcbond_it	9.208
r_dihedral_angle_2_deg	8.475
r_dihedral_angle_1_deg	6.744
r_angle_refined_deg	1.904
r_nbtor_refined	0.318
r_symmetry_nbd_refined	0.235
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.138
r_metal_ion_refined	0.133
r_symmetry_xyhbond_nbd_refined	0.083
r_ncsr_local_group_6	0.05
r_ncsr_local_group_10	0.049
r_ncsr_local_group_7	0.046
r_ncsr_local_group_3	0.045
r_ncsr_local_group_8	0.045
r_ncsr_local_group_5	0.043
r_ncsr_local_group_9	0.042
r_ncsr_local_group_4	0.041
r_ncsr_local_group_1	0.04
r_ncsr_local_group_2	0.04
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16190
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	162

Software

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