1M1N | pdb_00001m1n

Nitrogenase MoFe protein from Azotobacter vinelandii

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	PEG 8000, sodium chloride, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.31	α = 90
b = 131.63	β = 108.37
c = 159.159	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	CCD	ADSC QUANTUM 315		2002-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.992	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.16	100	95.6	0.09	0.078	10	2.5	1454519	1390520	1	1	12.34

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.16	1.18	90		0.535	0.554	1.6	2.5	65290

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3MIN	1.16	50	1454519	1376724	13733	95.61	0.12349	0.12323	0.14924	RANDOM	15.839

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]
0.26		1.13	-0.43		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.902
r_sphericity_free	9.996
r_sphericity_bonded	6.275
r_dihedral_angle_1_deg	5.831
r_scangle_it	5.698
r_scbond_it	4.054
r_mcangle_it	2.894
r_rigid_bond_restr	2.613
r_mcbond_it	2.258
r_angle_refined_deg	2.251
r_nbtor_other	1.049
r_angle_other_deg	1.039
r_symmetry_hbond_refined	0.828
r_symmetry_vdw_refined	0.396
r_xyhbond_nbd_other	0.382
r_symmetry_vdw_other	0.373
r_nbd_refined	0.333
r_nbd_other	0.263
r_xyhbond_nbd_refined	0.225
r_chiral_restr	0.163
r_bond_refined_d	0.029
r_gen_planes_refined	0.013
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32171
Nucleic Acid Atoms
Solvent Atoms	5021
Heterogen Atoms	192

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling