1Y07

Crystal structure of the superoxide reductase from Treponema pallidum

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG 3350, magnesium chloride, trisHCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.311	α = 90
b = 59.946	β = 104.96
c = 65.52	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 4	mirrors	2004-07-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	1.739, 1.033	ESRF	BM14

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	1.55	63.25	82.4	0.046	0.043	8.8	6.9	53624	53059	2	2	19.3

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)
	1.55	1.63	82.4		0.196	0.177	4.3	5.4	3751

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.55	63.25	2	2	53277	50599	2678	82.13	0.189	0.1845	0.18183	0.23522	RANDOM	14.824

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		0.26	1.66		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.328
r_sphericity_free	6.112
r_scangle_it	4.747
r_scbond_it	3.122
r_sphericity_bonded	2.47
r_mcangle_it	2.268
r_rigid_bond_restr	1.81
r_angle_refined_deg	1.765
r_mcbond_it	1.545
r_angle_other_deg	0.886
r_symmetry_vdw_other	0.357
r_symmetry_vdw_refined	0.334
r_nbd_other	0.261
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.188
r_chiral_restr	0.107
r_nbtor_other	0.088
r_bond_refined_d	0.02
r_gen_planes_other	0.02
r_gen_planes_refined	0.013
r_metal_ion_refined	0.012
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3724
Nucleic Acid Atoms
Solvent Atoms	356
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
CCP4	data scaling
PHENIX	phasing