8P1Z | pdb_00008p1z

Arabidopsis thaliana cytosolic seryl-tRNA synthetase in addition of dithiothreitol (DTT)

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, PEG 4000, TRIS pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.41	α = 90
b = 45.889	β = 93.942
c = 107.068	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		2019-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1	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	2.3	19.167	97.8	0.08	9.6	6		20826

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	2.3	2.39			0.816

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	2.3	19.158	20821	1080	97.728	0.229	0.2263	0.23	0.2888	0.29	50.999

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]
-0.001		0.006	0.001		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.965
r_dihedral_angle_3_deg	17.829
r_dihedral_angle_4_deg	14.015
r_dihedral_angle_1_deg	14.013
r_lrange_it	10.919
r_lrange_other	10.919
r_dihedral_angle_other_3_deg	6.524
r_scangle_it	6.345
r_scangle_other	6.344
r_mcangle_it	6.33
r_mcangle_other	6.329
r_mcbond_it	3.937
r_mcbond_other	3.937
r_scbond_it	3.847
r_scbond_other	3.846
r_angle_refined_deg	1.461
r_angle_other_deg	1.246
r_symmetry_nbd_refined	0.228
r_nbd_other	0.217
r_nbd_refined	0.197
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_other	0.154
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3256
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms

Software

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