2WLB | pdb_00002wlb

Adrenodoxin-like ferredoxin Etp1fd(516-618) of Schizosaccharomyces pombe mitochondria

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E6E	PDB ENTRIES 1E6E,1AYF,1L6V,2BT6
experimental model	PDB	1AYF	PDB ENTRIES 1E6E,1AYF,1L6V,2BT6
experimental model	PDB	1L6V	PDB ENTRIES 1E6E,1AYF,1L6V,2BT6
experimental model	PDB	2BT6	PDB ENTRIES 1E6E,1AYF,1L6V,2BT6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	277	VAPOUR DIFFUSION, SITTING DROP, 4 DEGR. CENTIGRADE. RESERVOIR: 0.04M HEPES,1.8M NA-CITRATE, 3% GLYCEROL,PH7.0. PROTEIN SOLUTION: 18.4MG/ML PROTEIN, 20MM POTASSIUMPHOSPHATE,PH7.4. 0.3 PLUS 0.3 MICROLITER DROPLET.

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.965	α = 90
b = 81.965	β = 90
c = 68.289	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	278	IMAGE PLATE	MAR scanner 345 mm plate		2004-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU H2B

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	2.6	20	99.5	0.11	8.5	3.4		8006			56.1

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	2.6	2.78	92.4		0.51	3.4	3.5

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1E6E,1AYF,1L6V,2BT6	2.6	20	8006	390	99.5	0.184	0.182	0.19	0.235	0.24	RANDOM	45.15

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]
0.31	0.16		0.31		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.132
r_dihedral_angle_3_deg	18.903
r_dihedral_angle_4_deg	13.795
r_scangle_it	9.292
r_scbond_it	6.76
r_dihedral_angle_1_deg	5.593
r_mcangle_it	3.93
r_mcbond_it	3.23
r_angle_refined_deg	1.453
r_angle_other_deg	0.915
r_symmetry_vdw_other	0.31
r_nbd_refined	0.215
r_nbd_other	0.202
r_symmetry_vdw_refined	0.2
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.147
r_nbtor_other	0.09
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	1567
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	8

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
SWISS-MODELLER	phasing
PHASER	phasing
REFMAC	refinement