1Y3T

Crystal structure of YxaG, a dioxygenase from Bacillus subtilis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GQG	PDB Entry 1GQG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	Sodium Hepes, PEG 400, Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.417	α = 90
b = 128.425	β = 90
c = 51.189	γ = 90

Symmetry
Space Group	P 21 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 QUANTUM 4		2002-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	20	98.2	0.089	20.37	6.01		33292	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.5	94.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry 1GQG	2.4	91.29	31547	1696	97.54	0.22013	0.21704	0.27679	RANDOM	37.9

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]
-0.99			-3.04		4.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	9.862
r_scangle_it	5.693
r_scbond_it	3.765
r_angle_refined_deg	2.996
r_mcangle_it	2.799
r_angle_other_deg	2.13
r_mcbond_it	1.691
r_nbd_other	0.323
r_symmetry_vdw_refined	0.313
r_nbd_refined	0.295
r_xyhbond_nbd_refined	0.284
r_symmetry_vdw_other	0.276
r_chiral_restr	0.211
r_gen_planes_other	0.162
r_nbtor_other	0.145
r_bond_other_d	0.13
r_gen_planes_refined	0.084
r_bond_refined_d	0.047
r_symmetry_hbond_refined	0.023

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5141
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	4

Software

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