2VKR | pdb_00002vkr

3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION			VAPOR DIFFUSION METHOD USING 2 MICROL DROPS OF FRESHLY PURIFIED PROTEIN AT 4.7 MG/ML IN 40 MM POTASSIUM PHOSPHATE PH 6.5 AND 150 NACL, PLUS 2 MICROL OF WELL SOLUTION, 2.4-3.0 M AMMONIUM SULPHATE BUFFERED WITH TRIS-HCL 0.1 M PH 8 AND 0.5 MICROL LAURYLDIMETHYLAMINE-OXIDE (LDAO) 7% (W/V).

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.5	α = 90
b = 117.5	β = 90
c = 50.9	γ = 120

Symmetry
Space Group	P 31

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 CCD		2002-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.01	19.48	99.2	0.08	9.9	2.2		52106

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	2.01	2.07	99.6		0.4	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FREE R-VALUE	PDB ENTRY 1XER	2.01	19.48	52097	2491	99.6	0.2148	0.2196		0.22	0.2729	0.23	THIN SHELLS

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
1		5395

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_adp_cmpnt	0.05
s_zero_chiral_vol	0.036
s_non_zero_chiral_vol	0.032
s_from_restr_planes	0.024
s_angle_d	0.018
s_anti_bump_dis_restr	0.007
s_bond_d	0.006
s_similar_dist	0.004
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5390
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	112

Software

Software
Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.