3P0H | pdb_00003p0h

Leishmania major Tyrosyl-tRNA synthetase in complex with fisetin, cubic crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J5B	Initial partial MR solution with PDB entry 2j5b, then determined experimental phases and heavy atom positions by SAD. Also used PDB entries 2cya and 2cyc to aid in model completion.
experimental model	PDB	2CYA	Initial partial MR solution with PDB entry 2j5b, then determined experimental phases and heavy atom positions by SAD. Also used PDB entries 2cya and 2cyc to aid in model completion.
experimental model	PDB	2CYC	Initial partial MR solution with PDB entry 2j5b, then determined experimental phases and heavy atom positions by SAD. Also used PDB entries 2cya and 2cyc to aid in model completion.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	equal volumes SeMet protein solution (24 mg/ml LmTyrRS in MSGPP buffer containing 5 mM DTT and 5 mM fisetin) and well solution (25% PEG 3350, 0.1 M tri-sodium citrate pH 5.5, and 4% w/v acetone); cryoprotected by addition of 30% PEG 3350, 10% MSGPP buffer, 10% ethylene glycol, and 0.1 M tri-sodium citrate pH 5.5 directly to drop prior to mounting and freezing crystals in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 240.24	α = 90
b = 240.24	β = 90
c = 240.24	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2010-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97931	SSRL	BL9-2

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	3	47.11	99.95	0.155	14.0489	13.81		46076			75

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	3	3.16	99.84		0.016		10.48	6696

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 (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, SAD	THROUGHOUT	Initial partial MR solution with PDB entry 2j5b, then determined experimental phases and heavy atom positions by SAD. Also used PDB entries 2cya and 2cyc to aid in model completion.	3	47.11	46076	2329	99.97	0.2355	0.2336	0.23	0.2727	0.27	RANDOM	80.8342

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.048
r_dihedral_angle_4_deg	15.338
r_dihedral_angle_3_deg	15.068
r_dihedral_angle_1_deg	4.873
r_scangle_it	3.615
r_mcangle_it	2.934
r_scbond_it	2.087
r_mcbond_it	1.702
r_angle_refined_deg	0.898
r_angle_other_deg	0.763
r_mcbond_other	0.236
r_chiral_restr	0.052
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9723
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	42

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
BALBES	phasing
PHASER	phasing