3HXY

Crystal Structure of catalytic fragment of E. coli AlaRS in complex with AMPPCP, Ala-AMP and PCP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	20% PEG 3350, 0.1 M Tris-HCl, 0.2 M Potassium Nitrate, pH 8.5, vapor diffusion, sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.355	α = 90
b = 108.745	β = 90
c = 118.985	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	MARMOSAIC 325 mm CCD		2008-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	2.27	50	100	0.037	65.368	10.1		27449

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)
1	2.27	2.35	99.9		0.085		10

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.27	41.56	26016	1374	99.94	0.1833	0.18095	0.22737	RANDOM	22.077

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]
-0.68			1.22		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.824
r_dihedral_angle_4_deg	13.82
r_dihedral_angle_3_deg	12.964
r_dihedral_angle_1_deg	5.71
r_scangle_it	4.008
r_mcangle_it	3.669
r_scbond_it	2.814
r_mcbond_it	2.561
r_angle_refined_deg	1.002
r_chiral_restr	0.364
r_nbtor_refined	0.321
r_nbd_refined	0.191
r_xyhbond_nbd_refined	0.177
r_symmetry_hbond_refined	0.163
r_symmetry_vdw_refined	0.148
r_metal_ion_refined	0.136
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3515
Nucleic Acid Atoms
Solvent Atoms	395
Heterogen Atoms	84

Software

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