3E1J

Crystal structure of E. coli Bacterioferritin (BFR) with an unoccupied ferroxidase centre (APO-BFR).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BCF	PDB ENTRY 1BCF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	1.8 M AMMONIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. CRYSTALS LATER SOAKED IN CRYOPROTECTANT AT PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, pH 5.00

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 208.216	α = 90
b = 208.216	β = 90
c = 142.457	γ = 90

Symmetry
Space Group	P 42 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				2006-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	35	98.8	0.101	14.5	6.5		84897		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.85	93.7		0.202	5	1.7

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 1BCF	2.7	35.11	80604	4239	98.7	0.243	0.242	0.263	RANDOM	6.29

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]
0.1			0.1		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.763
r_dihedral_angle_4_deg	22.581
r_dihedral_angle_3_deg	22.104
r_dihedral_angle_1_deg	4.689
r_scangle_it	3.354
r_scbond_it	2.07
r_angle_refined_deg	1.817
r_mcangle_it	1.138
r_mcbond_it	0.757
r_nbtor_refined	0.316
r_symmetry_hbond_refined	0.227
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.225
r_chiral_restr	0.17
r_xyhbond_nbd_refined	0.159
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15912
Nucleic Acid Atoms
Solvent Atoms	399
Heterogen Atoms	338

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling