8P1Y | pdb_00008p1y

Arabidopsis thaliana mutated variant C244S of seryl-tRNA synthetase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	magnesium chloride, TRIS pH 7, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.385	α = 90
b = 46.154	β = 93.791
c = 107.605	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 PILATUS 6M		2019-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.6	19.357	99.3	0.074	9.42	3.2		14883

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69			0.574

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	2.6	19.357	14881	764	99.299	0.211	0.20792	0.21	0.26577	0.26	59.162

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]
0.106		-0.043	0.012		-0.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.716
r_dihedral_angle_3_deg	17.065
r_dihedral_angle_4_deg	16.839
r_lrange_it	13.328
r_lrange_other	13.318
r_dihedral_angle_1_deg	8.292
r_scangle_it	8.151
r_scangle_other	8.151
r_mcangle_it	7.747
r_mcangle_other	7.746
r_scbond_it	4.948
r_scbond_other	4.946
r_mcbond_other	4.765
r_mcbond_it	4.764
r_angle_refined_deg	1.568
r_angle_other_deg	1.213
r_nbd_refined	0.218
r_symmetry_nbd_other	0.196
r_nbd_other	0.19
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.164
r_symmetry_nbd_refined	0.118
r_symmetry_xyhbond_nbd_refined	0.106
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.074
r_chiral_restr	0.06
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	3238
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
AMoRE	phasing