3H0L

Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GI3	PDB entries 2GI3 and 2G5H
experimental model	PDB	2G5H	PDB entries 2GI3 and 2G5H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1:1 ratio of Protein solution (6-9mg/ml GatCAB,10mM HEPES, 50uM Zn acetate,10mM Asn, 0.6mM ATP) mix with well solution (10-12% PEG3350, 10mM Mg formate), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.482	α = 90.02
b = 131.012	β = 90
c = 154.668	γ = 89.91

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD	MONOCHROMATOR: MIRRORS	2006-03-24	M	MAD
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	MONOCHROMATOR: MIRRORS	2007-03-20		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0274,0.9804	APS	23-ID-D
2	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97934	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.3	40.5	91.5	0.06	0.06	11.5	1.9	405875	405875

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.35	73.7		0.347	0.347	1.8	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 entries 2GI3 and 2G5H	2.3	40.5	405875	385553	20322	91.69	0.24169	0.24004	0.25	0.2726	0.28	RANDOM	50.929

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]
-4.63	-0.01	-0.26	9.07	0.04	-4.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.072
r_dihedral_angle_3_deg	18.656
r_dihedral_angle_4_deg	17.933
r_dihedral_angle_1_deg	6.149
r_scangle_it	2.305
r_scbond_it	1.454
r_angle_refined_deg	1.396
r_mcangle_it	1.11
r_mcbond_it	0.672
r_nbtor_refined	0.309
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.215
r_symmetry_hbond_refined	0.206
r_xyhbond_nbd_refined	0.166
r_metal_ion_refined	0.098
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
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	62848
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	296

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling