3EZ0 | pdb_00003ez0

Crystal structure of protein of unknown function with ferritin-like fold (YP_832262.1) from Arthrobacter sp. FB24 at 2.33 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.47	293	20.0% polyethylene glycol 3350, 0.171M potassium sodium tartrate, 0.1M MES pH 6.47, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.6	α = 90
b = 96.71	β = 97.6
c = 71.2	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-08-11	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)	Rrim I (All)	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	2.33	29.54	97.4	0.067	0.083	10.67	5.65		35863		-3	46.71

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.33	2.41	96.2		0.612	0.755	1.85

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	2.33	29.54	35842	1786	99.54	0.213	0.21	0.21	0.262	0.27	RANDOM	46.715

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]
0.28		0.18	-0.34		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.164
r_dihedral_angle_4_deg	15.697
r_dihedral_angle_3_deg	15.173
r_scangle_it	6.645
r_scbond_it	4.679
r_dihedral_angle_1_deg	3.592
r_mcangle_it	2.749
r_mcbond_it	1.657
r_angle_refined_deg	1.304
r_angle_other_deg	0.941
r_mcbond_other	0.371
r_symmetry_vdw_other	0.247
r_symmetry_vdw_refined	0.214
r_nbd_refined	0.202
r_nbd_other	0.185
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.165
r_symmetry_hbond_refined	0.138
r_nbtor_other	0.089
r_chiral_restr	0.07
r_bond_refined_d	0.013
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	6583
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	98

Software

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