2ZZF | pdb_00002zzf

Crystal structure of alanyl-tRNA synthetase without oligomerization domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RIQ	1RIQ, 1V7O
experimental model	PDB	1V7O	1RIQ, 1V7O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.6	293	PEG6000, MES, succinic acid, glucose, pH 5.6, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.258	α = 90
b = 98.84	β = 108.64
c = 72.927	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 210	mirrors	2006-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

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	2.7	50	98.5	0.05	44.059	5.3		29921			85.4

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)
	2.7	2.8	88.1		0.286		4	2667

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	1RIQ, 1V7O	2.7	30.15	29902	1506	98.5	0.208	0.206	0.2237	0.263	0.2223	RANDOM	75.929

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]
-0.38		-0.2	0.27		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.542
r_dihedral_angle_3_deg	19.599
r_dihedral_angle_4_deg	17.301
r_dihedral_angle_1_deg	6.21
r_scangle_it	2.631
r_scbond_it	1.566
r_angle_refined_deg	1.454
r_mcangle_it	1.162
r_mcbond_it	0.674
r_nbtor_refined	0.313
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.162
r_symmetry_vdw_refined	0.152
r_symmetry_hbond_refined	0.124
r_chiral_restr	0.106
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_metal_ion_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5926
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	2

Software

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