2ZZE | pdb_00002zze

Crystal structure of alanyl-tRNA synthetase without oligomerization domain in lysine-methylated form

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	PEG 4000, ammonium acetate, tri-sodium citrate, pH 5.6, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.063	α = 90
b = 130.151	β = 117.46
c = 94.855	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	ADSC QUANTUM 315	mirrors	2008-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU

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	2.15	50	98.2	0.068	21.411	3.9	102794	100967			29.1

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)
	2.15	2.23	97.1		0.343		3.8	9921

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	2.16	38.58	100932	5088	97.96	0.191	0.189	0.217	0.227	0.215	RANDOM	24.6

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.587
r_dihedral_angle_4_deg	17.468
r_dihedral_angle_3_deg	14.85
r_dihedral_angle_1_deg	5.777
r_scangle_it	1.835
r_angle_refined_deg	1.125
r_scbond_it	1.116
r_mcangle_it	0.768
r_mcbond_it	0.467
r_nbtor_refined	0.304
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.173
r_symmetry_hbond_refined	0.124
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12280
Nucleic Acid Atoms
Solvent Atoms	843
Heterogen Atoms	2

Software

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