Experiment: 6VXT

Activated Nitrogenase MoFe-protein from Azotobacter vinelandii

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U7Q	PDB entry 3U7Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	14-19 % w/v PEG smear high, 0.16 M ammonium acetate, 0.1 M sodium citrate(pH 5.0), 25.6 % v/v glycerol, 5 mM sodium dithionite

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.535	α = 90
b = 203.435	β = 103.945
c = 83.857	γ = 90

Symmetry
Space Group	C 1 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	PIXEL	DECTRIS PILATUS 6M		2019-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	1.0000	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.73	50	96.8	0.15	0.06	0.989	17.4	6.1		263634			32.39

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.76	71.9		0.97	0.322		4

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 3U7Q	1.74	41.71	1.34	262041	1983	96.1	0.1726	0.1724	0.1732	0.2029	0.2034	44.19

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	9.284
f_angle_d	0.8507
f_chiral_restr	0.0528
f_bond_d	0.007
f_plane_restr	0.0055

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15617
Nucleic Acid Atoms
Solvent Atoms	1234
Heterogen Atoms	148

Software

Software
Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing