2JD7 | pdb_00002jd7

Crystal Structure of the Fe-soaked Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus furiosus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JD6	REFINED 2JD6 COORDINATES

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				THE CRYSTALS USED FOR DATA COLLECTION WERE GROWN AGAINST 0.5 ML OF 2 M AMMONIUM SULPHATE RESERVOIR SOLUTION, WITH DROPS CONTAINING 2 MICRO-L OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 AND EQUAL AMOUNT OF THE RESERVOIR SOLUTION. IRON SOAKING OF FERRITIN CRYSTALS WAS PERFORMED BY TRANSFERRING THEM TO A 10-20 MICRO-L DROP OF A SOLUTION WITH COMPOSITION 20 MM FESO4, 2 MM NA2S2O4, 25 % GLYCEROL AND 2 M AMMONIUM SULFATE, FOR 15 MINUTES.

Crystal Properties
Matthews coefficient	Solvent content
4	69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 254.301	α = 90
b = 342.878	β = 90
c = 266.221	γ = 90

Symmetry
Space Group	C 2 2 21

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	MARRSEARCH	COLLIMATING AND FOCUSSING MIRRO	2006-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.8	42	99.1	0.08	8.2	3.6		280407			60.5

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	2.8	2.95	94.1		0.35	2	2.6

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	REFINED 2JD6 COORDINATES	2.8	204.12	266173	14187	99.1	0.201	0.199	0.25	RANDOM	39.42

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]
1.52			-1.4		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.271
r_dihedral_angle_3_deg	19.208
r_dihedral_angle_4_deg	17.239
r_scangle_it	7.241
r_dihedral_angle_1_deg	5.469
r_scbond_it	4.847
r_mcangle_it	3.374
r_mcbond_it	2.084
r_angle_refined_deg	1.467
r_nbtor_refined	0.32
r_nbd_refined	0.23
r_symmetry_vdw_refined	0.21
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
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_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	49788
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	238

Software

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