3M4P | pdb_00003m4p

Entamoeba histolytica asparaginyl-tRNA synthetase (AsnRS) in complex with asparaginyl-adenylate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X56	1x56, protein only model prepared using CHAINSAW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	1 ul 22 mg/ml protein in SGPP buffer mixed with 1 ul well soln. (100 mM Bis-Tris pH 5.5, 28% PEG 3350, 240 mM ammonium sulfate), drop supplemented with 10 mM L-asparagine + 10 mM ATP + 10 mM MgCl2 + 5 mM DTT; cryoprotected by quick dip in well soln containing 30% PEG 3350 and supplemented with 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.426	α = 90
b = 58.816	β = 90.45
c = 181.259	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 325 mm CCD		2009-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	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	2.83	50	100	0.062	14.9	4.6		50783		3	73

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)
	2.83	2.93	100		0.459	2.7	4.6	5048

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	THROUGHOUT	1x56, protein only model prepared using CHAINSAW	2.83	41.36	50772	2577	99.79	0.202	0.199	0.2	0.247	0.24	RANDOM	75.533

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]
4.52		-1.73	0.19		-4.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.165
r_dihedral_angle_4_deg	17.763
r_dihedral_angle_3_deg	14.71
r_dihedral_angle_1_deg	5.651
r_scangle_it	2.884
r_scbond_it	1.796
r_mcangle_it	1.641
r_angle_refined_deg	0.985
r_mcbond_it	0.902
r_angle_other_deg	0.772
r_mcbond_other	0.24
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13902
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	196

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling