8FBZ

Crystal Structure of apo human Glutathione Synthetase Y270E

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HGS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	HEPES, PEG400, ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.834	α = 90
b = 94.051	β = 92.522
c = 125.122	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	PIXEL	DECTRIS PILATUS3 S 2M		2022-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0	ALS	8.2.2

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	1.59	47.07	98.6	0.093	0.106	0.066	0.996	10.1	4.3		123489

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	1.59	1.63			0.687	0.778	0.359	0.74	2.1

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.59	47.07	123427	6675	98.42	0.161	0.1599	0.1888	20.175

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]
1.139		0.073	-0.899		-0.245

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.596
r_dihedral_angle_4_deg	17.62
r_dihedral_angle_3_deg	12.644
r_lrange_it	7.894
r_lrange_other	7.672
r_scangle_it	6.37
r_scangle_other	6.369
r_dihedral_angle_1_deg	6.128
r_scbond_it	4.33
r_scbond_other	4.33
r_mcangle_other	2.96
r_mcangle_it	2.958
r_mcbond_it	2.136
r_mcbond_other	2.131
r_angle_other_deg	1.375
r_angle_refined_deg	1.357
r_symmetry_nbd_refined	0.239
r_nbd_refined	0.196
r_nbd_other	0.185
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.146
r_symmetry_xyhbond_nbd_refined	0.144
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.077
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7186
Nucleic Acid Atoms
Solvent Atoms	1046
Heterogen Atoms	36

Software

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