9SPZ | pdb_00009spz

Crystal structure of the Molybdenum-containing nitrogenase from Methanocaldococcus infernus refined to 1.37 A resolution - crystalline form A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293.15	Samples were centrifuged at 13,000 x g for 3 min to remove macro-aggregates and dust, and crystallised inside an anaerobic chamber (N2/H2 (97:3%) atmosphere, 20 degrees Celsius). Crystallisation was done by the sitting drop method in 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) plate containing 90 uL of crystallisation solution in the reservoir in all cases. Crystals were obtained by mixing 0.7 uL of crystallisation solution with 0.7 uL of protein sample at a concentration of 2.95 mg/mL. The crystallisation solution contained the following: 30 % v/v 2-methyl-2,4-pentanediol, 100 mM Tris pH 8.5, 500 mM Sodium chloride, and 8 % w/v Polyethylene glycol 8,000 (Crystallisation solution of the JBScreen Wizard form Jena Bioscience, Germany).

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.433	α = 90
b = 117.18	β = 91.48
c = 106.627	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2022-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00000	SLS	X06SA

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	1.37	78.85	95.3	0.091	0.096	0.029	0.998	12.3	10.4		273586

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	1.37	1.515	68.2		1.198	1.266	0.404	0.658	1.9	9.6

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	1.37	21.91	1.34	273457	13619	67.94	0.1249	0.1233	0.1245	0.1556	0.1557

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	15.394
f_angle_d	1.262
f_chiral_restr	0.877
f_plane_restr	0.013
f_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14915
Nucleic Acid Atoms
Solvent Atoms	1454
Heterogen Atoms	233

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing