2GJ3 | pdb_00002gj3

Crystal structure of the FAD-containing PAS domain of the protein NifL from Azotobacter vinelandii.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	2.25M Ammonium sulfate, 5% ethanol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.111	α = 90
b = 68.111	β = 90
c = 302.064	γ = 120

Symmetry
Space Group	H 3 2

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	MAR CCD 165 mm			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	0.8266	APS	14-ID-B

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	1.03	50	94.5	0.04	14.3			126308

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)
	1.03	1.07	50	63.1	0.462

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.04	40	126308	115137	11569	88.65	0.158	0.158	0.154	0.16	0.186	0.17	RANDOM	21.636

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]
-0.65	-0.33		-0.65		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.166
r_dihedral_angle_4_deg	23.102
r_sphericity_free	18.576
r_dihedral_angle_3_deg	13.581
r_sphericity_bonded	11.24
r_dihedral_angle_1_deg	11.173
r_scangle_it	6.926
r_mcangle_it	5.926
r_scbond_it	5.692
r_mcbond_it	5.1
r_rigid_bond_restr	4.505
r_angle_refined_deg	3.458
r_symmetry_hbond_refined	0.381
r_nbtor_refined	0.324
r_nbd_refined	0.282
r_xyhbond_nbd_refined	0.272
r_symmetry_vdw_refined	0.249
r_chiral_restr	0.192
r_bond_refined_d	0.027
r_gen_planes_refined	0.024

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1920
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	126

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SOLVE	phasing