8Q5V | pdb_00008q5v

MgADP-bound Fe protein of the molybdenum nitrogenase from Methanothermococcus thermolithotrophicus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8Q50

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293.15	The purified protein was crystallised at a final concentration of 32.7 mg/ml with 10 mM ATP and 10 mM MgCl2 by spotting 0.5 ul of crystallisation solution with 0.5 ul of protein sample. Crystallisation was done anaerobically in a Coy tent containing N2/H2 (97:3%) atmosphere. The screening was done at 20 degrees Celsius on 96-Well MRC 2-drop polystyrene (SWISSCI) plates containing 90 ul of crystallisation solution. The crystallisation solution in which crystals were obtained contained 20 % w/v polyethylene glycol 8000, 100 mM Tris pH 8.5 and 200 mM magnesium chloride. The crystals were soaked in the crystallisation solution supplemented with 30% glycerol prior freezing in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.478	α = 93.98
b = 87.594	β = 98.58
c = 182.048	γ = 109.65

Symmetry
Space Group	P 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 2M-F		2020-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00004	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.74	71	90.5	0.284	0.307	0.117	0.983	4.5	6.7		66142

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.74	2.9	63.1		1.224	1.358	0.509	0.526	1.6	6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.74	39.93	1.96	66105	3242	72.08	0.219	0.2172	0.216	0.2543	0.2521	60.62

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	15.84
f_angle_d	1.239
f_chiral_restr	0.085
f_bond_d	0.009
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25495
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	462

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	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.