2VZB

A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein from Bacteroides fragilis

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		0.1 M BIS-TRIS HCL PH 8.5, 0.25 M MGCL2, 16 % (W/V) PEG 4,000, 2 % (W/V) BENZAMIDINE HCL, 20 % GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.34	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.695	α = 90
b = 129.695	β = 90
c = 129.695	γ = 90

Symmetry
Space Group	P 21 3

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 CCD		2007-03-12	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	2.3	37	99.6	0.08	17.5	3.6		34431		2

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	99.4		0.24	2.9	1.9

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	PDB ENTRY 2CLB	2.3	37	30759	1629	99.5	0.197	0.195	0.224	RANDOM	34.86

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.984
r_dihedral_angle_4_deg	14.625
r_dihedral_angle_3_deg	14.13
r_dihedral_angle_1_deg	4.684
r_angle_other_deg	2.52
r_scangle_it	2.155
r_scbond_it	1.527
r_angle_refined_deg	1.152
r_mcangle_it	0.847
r_mcbond_it	0.842
r_symmetry_vdw_other	0.315
r_nbd_refined	0.222
r_nbd_other	0.203
r_symmetry_vdw_refined	0.177
r_nbtor_refined	0.176
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.168
r_nbtor_other	0.083
r_chiral_restr	0.063
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5413
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
COMO	phasing