4O2D | pdb_00004o2d

Crystal structure of aspartyl-tRNA synthetase from Mycobacterium smegmatis with bound aspartic acid

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	289	20% PEG 3350, 0.2M Na Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.4	α = 90
b = 135.17	β = 90
c = 157.05	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	100	CCD	RAYONIX MX300HE		2013-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	42.72	99.8	0.072	23.9	5.8	51452	51363			35.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	99.9		0.499	4.5	6	3761

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	PDB ENTRY 1EQR	2.6	42.72	48854	2559	99.83	0.19785	0.19548	0.2	0.24361	0.25	RANDOM	49.356

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]
2.21			1.52		-3.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.649
r_dihedral_angle_4_deg	17.526
r_dihedral_angle_3_deg	13.733
r_dihedral_angle_1_deg	7.121
r_long_range_B_refined	4.675
r_long_range_B_other	4.675
r_mcangle_other	2.414
r_mcangle_it	2.413
r_scangle_other	2.397
r_angle_refined_deg	1.594
r_scbond_it	1.535
r_scbond_other	1.533
r_mcbond_it	1.449
r_mcbond_other	1.437
r_angle_other_deg	1
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8163
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	50

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling