1ZH0

Crystal Structure of L-3-(2-napthyl)alanine-tRNA synthetase in complex with L-3-(2-napthyl)alanine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20% PEG-300, 5% PEG-8000,10% glycerol 0.1M Tris, pH 8.5, vapor diffusion,sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.995	α = 90
b = 102.995	β = 90
c = 71.441	γ = 90

Symmetry
Space Group	P 43 21 2

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		2004-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0	ALS	5.0.3

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	1.9	72.74	93.7	0.053		2.9	28143	33956

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2.03	93.2	78.1		1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	72.74	28143	28143	1507	96.09	0.222	0.222	0.22	0.275	RANDOM	50.724

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]
1.35			1.35		-2.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.888
r_dihedral_angle_3_deg	18.396
r_dihedral_angle_4_deg	15.731
r_scangle_it	6.357
r_dihedral_angle_1_deg	6.112
r_scbond_it	5.243
r_mcangle_it	2.483
r_mcbond_it	1.724
r_angle_refined_deg	1.574
r_angle_other_deg	1.099
r_symmetry_hbond_refined	0.448
r_nbd_refined	0.217
r_mcbond_other	0.216
r_symmetry_vdw_other	0.194
r_xyhbond_nbd_refined	0.192
r_nbd_other	0.184
r_nbtor_refined	0.183
r_xyhbond_nbd_other	0.157
r_chiral_restr	0.116
r_symmetry_vdw_refined	0.1
r_nbtor_other	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2461
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	24

Software

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