7YSE

Crystal structure of E. coli heterotetrameric GlyRS in complex with tRNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		281	0.15M MgCl2, 0.1M NaCl, 0.1M Tris-HCl pH 8.5, 30% PEG 300

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.71	α = 90
b = 162.123	β = 90
c = 324.09	γ = 90

Symmetry
Space Group	P 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 16M		2021-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.979	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.907	162.12	100	0.138	0.059	0.99	9.4	6.6		85473

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.907	3.06			0.749	0.304	0.774

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	7eiv, 4mgm	2.907	50.005	85392	4393	99.885	0.231	0.2296	0.2598	77.244

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]
6.585			-2.903		-3.682

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.037
r_dihedral_angle_4_deg	18.004
r_dihedral_angle_3_deg	16.983
r_lrange_it	5.745
r_lrange_other	5.745
r_dihedral_angle_1_deg	5.556
r_scangle_it	3.494
r_scangle_other	3.493
r_mcangle_other	3.475
r_mcangle_it	3.474
r_mcbond_it	2.073
r_mcbond_other	2.073
r_scbond_it	2.068
r_scbond_other	2.068
r_angle_refined_deg	1.231
r_angle_other_deg	1.171
r_symmetry_nbd_other	0.193
r_nbd_refined	0.184
r_nbd_other	0.173
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.097
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.06
r_symmetry_nbd_refined	0.059
r_chiral_restr	0.051
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14340
Nucleic Acid Atoms	2952
Solvent Atoms	14
Heterogen Atoms	62

Software

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