3F90 | pdb_00003f90

Desulfovibrio desulfuricans (ATCC 29577) semiquinone flavodoxin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F6S	PDB entry 3F6S oxidized Desulfovibrio desulfuricans (ATCC 29577) flavodoxin

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.2M postassium thiocyanate, 2.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.893	α = 90
b = 94.893	β = 90
c = 238.09	γ = 120

Symmetry
Space Group	P 31 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	100	IMAGE PLATE	RIGAKU RAXIS IV++	Rigaku Varimax HF	2008-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54

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	2.5	20	91.8	0.084	10.7	5	40326	40270		3

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)
	2.5	2.59	61.7		0.194	4.2	2.7	2657

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 entry 3F6S oxidized Desulfovibrio desulfuricans (ATCC 29577) flavodoxin	2.5	19.889	1.33	40270	4148	91.76	0.2573	0.2539	0.2551	0.2885	0.285	random	48.855

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]
-10.18			-10.18		-18.92

RMS Deviations
Key	Refinement Restraint Deviation
f_angle_deg	0.863
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8744
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	248

Software

Software
Software Name	Purpose
PHENIX	refinement
PHASER	phasing
CNS	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling