4J75 | pdb_00004j75

Crystal Structure of a parasite tRNA synthetase, product-bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4J76	PDB ENTRY 4J76

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2 M sodium citrate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.033	α = 90
b = 189.473	β = 90
c = 51.45	γ = 90

Symmetry
Space Group	P 21 21 2

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	RIGAKU SATURN 944		2010-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	2.4	38.64	99.2	0.171	12.5	7.3		45354

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	2.4	2.48	98.2		0.01	2.2	7.4	4348

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4J76	2.4	30	45312	2309	98.96	0.1944	0.1929	0.2225	0.1881	RANDOM	43.9496

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]
0.18			-0.41		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.034
r_dihedral_angle_4_deg	18.391
r_dihedral_angle_3_deg	14.43
r_dihedral_angle_1_deg	5.759
r_mcangle_it	1.235
r_angle_refined_deg	1.165
r_angle_other_deg	0.911
r_mcbond_it	0.711
r_mcbond_other	0.709
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6073
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	86

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction