2PID | pdb_00002pid

Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VBM	PDB ENTRY 1VBM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	293	3 mg/ml protein, 30% (m/v) PEG 4000, 200 mM Ammonium acetate, 100 mM sodium acetate pH 4.6, 100 mM Tris-HCl pH 7.5, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54	α = 90
b = 62.4	β = 90
c = 194.6	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 315		2006-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	20	99.5	0.098	0.098	19.1	11.8		34168		-3	39.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.3	100		0.427	0.427	8.2	12.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1VBM	2.2	19.98	34156	34156	1700	99.6	0.193	0.193	0.19	0.244	0.24	RANDOM	40.4

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]
7.6			3.12		-10.72

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.7
c_scangle_it	5.8
c_scbond_it	4.2
c_mcangle_it	3.84
c_mcbond_it	2.83
c_improper_angle_d	1.71
c_angle_deg	1.4
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5102
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	70

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing