3DDE

Crystal structure of a domain of unknown function with a heme oxygenase-like fold (sden_3740) from shewanella denitrificans os217 at 2.30 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	20.0% polyethylene glycol 3350, 0.269M magnesium nitrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.81	α = 90
b = 66	β = 90
c = 84.38	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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-03-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97932,0.97918	SSRL	BL9-2

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	29.173	97.6	0.041	12.6			23523		-3	47.797

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	2.38	88.8		0.433	1.9

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	MAD	THROUGHOUT	2.3	29.173	23503	1206	99.36	0.221	0.22	0.253	RANDOM	42.692

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]
3.08			-1.74		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.655
r_dihedral_angle_4_deg	19.04
r_dihedral_angle_3_deg	11.435
r_dihedral_angle_1_deg	2.884
r_angle_refined_deg	1.34
r_scangle_it	1.028
r_angle_other_deg	1.001
r_mcangle_it	1.001
r_scbond_it	0.7
r_mcbond_it	0.679
r_symmetry_vdw_other	0.264
r_mcbond_other	0.26
r_nbd_refined	0.21
r_nbtor_refined	0.183
r_nbd_other	0.169
r_symmetry_hbond_refined	0.169
r_symmetry_vdw_refined	0.151
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.09
r_nbtor_other	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3555
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	39

Software

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