3K1A | pdb_00003k1a

Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70Ile MoFe protein variant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2MIN	PDB entry 2MIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	8	298	30% PEG 4000, 100mM Tris-HCl pH 8.0, 170-190mM Sodium molybdate and 1mM Dithionite, LIQUID DIFFUSION, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.019	α = 90
b = 129.458	β = 109.01
c = 107.088	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	MARMOSAIC 325 mm CCD	mirrors	2008-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.8900	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.23	50	99.9	0.115	11.8	3.8		187881		2.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.23	2.33			0.233		3.5	18797

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	PDB entry 2MIN	2.23	50	90665	4778	98.46	0.207	0.20449	0.21	0.25433	0.26	RANDOM	31.399

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]
1.66		0.38	0.23		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.469
r_dihedral_angle_4_deg	24.593
r_dihedral_angle_3_deg	15.597
r_scangle_it	7.743
r_dihedral_angle_1_deg	5.811
r_scbond_it	5.386
r_angle_refined_deg	3.226
r_mcbond_it	2.29
r_mcangle_it	2.138
r_angle_other_deg	1.279
r_mcbond_other	0.372
r_xyhbond_nbd_other	0.237
r_symmetry_vdw_other	0.231
r_symmetry_vdw_refined	0.213
r_symmetry_hbond_refined	0.194
r_nbd_other	0.191
r_nbd_refined	0.19
r_nbtor_refined	0.173
r_metal_ion_refined	0.167
r_xyhbond_nbd_refined	0.142
r_nbtor_other	0.082
r_chiral_restr	0.06
r_bond_refined_d	0.011
r_bond_other_d	0.007
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15778
Nucleic Acid Atoms
Solvent Atoms	830
Heterogen Atoms	96

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling