3E6S | pdb_00003e6s

Crystal structure of ferritin soaked with iron from Pseudo-nitzschia multiseries

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	Crystals grown in 0.1 M ammonium acetate pH 5.5 and 1.6 M ammonium sulphate then soaked in 20 mM ferrous sulphate, 2 mM sodium sulphate and 25% glycerol for 10 minutes, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.625	α = 90
b = 125.625	β = 90
c = 170.132	γ = 90

Symmetry
Space Group	P 4 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	90	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, double crystal monochromator, toroid focusing mirror	2008-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9200	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	1.95	50	99.8	0.064		6.9	99333	99298			29.745

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)
	1.95	2.02	100		0.463		6.3	9816

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 (All)	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		THROUGHOUT	1.95	35.22	99298	4959	99.73	0.172	0.172	0.17	0.17	0.205	0.21	RANDOM	27.347

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]
0.37			0.37		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.549
r_dihedral_angle_4_deg	14.295
r_dihedral_angle_3_deg	13.387
r_scangle_it	5.621
r_dihedral_angle_1_deg	4.483
r_scbond_it	3.437
r_mcangle_it	1.89
r_angle_refined_deg	1.414
r_mcbond_it	1.164
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.257
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.208
r_xyhbond_nbd_refined	0.196
r_symmetry_metal_ion_refined	0.171
r_metal_ion_refined	0.116
r_chiral_restr	0.107
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7687
Nucleic Acid Atoms
Solvent Atoms	881
Heterogen Atoms	37

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing