3HZR | pdb_00003hzr

Tryptophanyl-tRNA synthetase homolog from Entamoeba histolytica

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FOC	PDB ENTRY 3FOC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	0.2 M Sodium Citrate, 20% PEG 3350, 1mM TCEP, 10 mM Zn, pH 7.0, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.2	α = 90
b = 158.88	β = 107.33
c = 100.28	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	IMAGE PLATE	MAR scanner 345 mm plate		2008-07-15		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	3	47.891	97.7	0.115	0.115	5.609	3.2		54415			85

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	3	3.16	98.8		0.01	1.046	0.7	3.1	7976

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 3FOC	3	47.89	54396	2753	97.58	0.229	0.228	0.25	0.2677	RANDOM	20.134

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]
0.14		-2.73	-3.69		1.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.508
r_dihedral_angle_4_deg	21.671
r_dihedral_angle_3_deg	18.222
r_dihedral_angle_1_deg	7.144
r_angle_refined_deg	1.361
r_angle_other_deg	0.924
r_chiral_restr	0.072
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17738
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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