5KOH | pdb_00005koh

Nitrogenase MoFeP from Gluconacetobacter diazotrophicus in dithionite reduced state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M1N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	45% 2-methyl-2,4-pentadiol (MPD) , 300 mM NaCl, 100 mM Na Cacodylate, pH 6.5, 1 mM Spermine, 0.1% Zwittergent, and 5 mM Na2S2O4

Crystal Properties
Matthews coefficient	Solvent content
3	59.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 202.598	α = 90
b = 202.598	β = 90
c = 132.567	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	PIXEL	DECTRIS PILATUS 6M		2016-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.98	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.83	143.26	100	0.4208	0.4288	0.976	12.85	27.2		240200			14.27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.895	100		1.434	0.815	1.46	27.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	1M1N	1.83	143.26	228228	11943	99.97	0.12972	0.12864	0.1421	0.15039	0.1625	RANDOM	17.981

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]
-0.37			-0.37		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.23
r_dihedral_angle_4_deg	18.405
r_dihedral_angle_3_deg	13.226
r_long_range_B_refined	6.714
r_long_range_B_other	6.235
r_dihedral_angle_1_deg	6.132
r_scangle_other	4.705
r_scbond_it	3.091
r_scbond_other	3.091
r_angle_refined_deg	2.015
r_mcangle_it	2.014
r_mcangle_other	2.014
r_angle_other_deg	1.79
r_mcbond_it	1.455
r_mcbond_other	1.455
r_chiral_restr	0.148
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.007
r_gen_planes_other	0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15640
Nucleic Acid Atoms
Solvent Atoms	1979
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data scaling
Aimless	data scaling
PHASER	phasing