2IIZ

Crystal structure of putative melanin biosynthesis protein TyrA with bound heme (NP_716371.1) from Shewanella Oneidensis at 2.30 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HAG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	287	0.1M Tris, 5% isopropyl alcohol, 20% (w/v) polyethylene glycol 4000, additive - 1mM hemin, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
3.58	65.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.837	α = 90
b = 94.837	β = 90
c = 116.666	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 QUANTUM 315	Flat mirror (vertical focusing)	2006-07-31	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	2.3	19.9	99.7	0.142	11.72	6.95		24210			38.592

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	2.3	2.45	100		0.552	3		4094

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	2HAG	2.3	19.8	24207	1269	99.88	0.208	0.205	0.266	RANDOM	33.304

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]
-1.39			-1.39		2.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.049
r_dihedral_angle_4_deg	16.274
r_dihedral_angle_3_deg	13.869
r_dihedral_angle_1_deg	6.456
r_scangle_it	5.78
r_scbond_it	4.387
r_mcangle_it	2.281
r_angle_refined_deg	1.357
r_mcbond_it	1.33
r_angle_other_deg	0.763
r_mcbond_other	0.329
r_symmetry_hbond_refined	0.292
r_symmetry_vdw_refined	0.255
r_symmetry_vdw_other	0.24
r_nbd_refined	0.203
r_nbd_other	0.19
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.134
r_nbtor_other	0.087
r_chiral_restr	0.076
r_bond_refined_d	0.013
r_bond_other_d	0.002
r_gen_planes_refined	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2441
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	56

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
MolProbity	model building
PDB_EXTRACT	data extraction
XDS	data reduction