3QZB | pdb_00003qzb

Crystal structure of a putative superoxide reductase (TM0658) from THERMOTOGA MARITIMA at 1.10 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	277	32.70% polyethylene glycol 3000, 0.1M CHES pH 9.0, Additive: 0.001 M cytidine monophosphate (CMP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.26	α = 90
b = 54.63	β = 90
c = 88.84	γ = 90

Symmetry
Space Group	I 2 2 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	double crystal monochromator	2009-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		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	1.1	28.771	98.3	0.062	13.15			51057		-3	6.511

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	1.1	1.14	96.1		0.537	2.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.1	28.771	51057	2594	98.34	0.1259	0.1244	0.13	0.1534	0.16	RANDOM	11.7974

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]
-0.24			0.61		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.801
r_dihedral_angle_4_deg	21.402
r_dihedral_angle_3_deg	11.387
r_sphericity_free	10.529
r_dihedral_angle_1_deg	6.893
r_scangle_it	5.793
r_scbond_it	4.226
r_sphericity_bonded	4.05
r_mcangle_it	3.423
r_mcbond_it	2.536
r_rigid_bond_restr	2.112
r_angle_refined_deg	1.804
r_mcbond_other	1.607
r_angle_other_deg	1.031
r_chiral_restr	0.122
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1058
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	1

Software

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