2Z8Q | pdb_00002z8q

ferredoxin from Pyrococcus furiosus, D14C variant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SJ1	pdb entry 1sj1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	35% PEG 600, 0.1 MIB pH 7.5, 7mM [Co(NH3)6]Cl3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.4	α = 90
b = 116.8	β = 90
c = 47.7	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	ADSC QUANTUM 4		2006-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	36.94	99.9	0.112	0.112	11.41	7	16226	16226

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.8	100		0.258	0.258	5	7	2509

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1sj1	1.7	26.01	15399	15399	811	99.96	0.1656	0.1656	0.1641	0.1615	0.19396	0.1888	RANDOM	13.535

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]
-0.66			0.53		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.738
r_dihedral_angle_3_deg	13.63
r_dihedral_angle_1_deg	5.145
r_scangle_it	4.598
r_mcangle_it	3.404
r_scbond_it	3.093
r_mcbond_it	2.367
r_angle_refined_deg	1.292
r_nbtor_refined	0.311
r_nbd_refined	0.232
r_symmetry_hbond_refined	0.209
r_xyhbond_nbd_refined	0.198
r_symmetry_vdw_refined	0.187
r_chiral_restr	0.103
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	988
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing