9HBC | pdb_00009hbc

A. vinelandii nitrogenase MoFe protein Anc2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U7Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	4.5% (w/v) of polyethylene glycol 2000, 3350, 4000 and polyethylene glycol mono methylether 5000, 0.1 M MES/NaOH at pH 6.5, 10% (v/v) of ethylene glycol and 0.15 M Mg acetate

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.936	α = 90
b = 130.133	β = 90
c = 209.137	γ = 90

Symmetry
Space Group	P 21 21 21

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		2022-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.816	110.49	95	0.2	0.998	10	13		121997

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.816	2.013			1.642	0.478	0.698

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.816	110.489	121997	6145	66.086	0.179	0.1762	0.1848	0.2254	0.2287	RANDOM	25.546

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]
0.191			0.073		-0.264

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.499
r_dihedral_angle_3_deg	13.474
r_dihedral_angle_other_3_deg	9.043
r_dihedral_angle_2_deg	7.342
r_dihedral_angle_1_deg	6.796
r_lrange_it	5.864
r_lrange_other	5.782
r_scangle_it	4.539
r_scangle_other	4.539
r_mcangle_it	3.338
r_mcangle_other	3.338
r_scbond_it	2.905
r_scbond_other	2.905
r_mcbond_it	2.259
r_mcbond_other	2.259
r_angle_refined_deg	1.638
r_angle_other_deg	0.57
r_nbd_other	0.23
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.195
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.174
r_symmetry_xyhbond_nbd_other	0.129
r_metal_ion_refined	0.102
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_1	0.061
r_ncsr_local_group_2	0.049
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15926
Nucleic Acid Atoms
Solvent Atoms	1298
Heterogen Atoms	112

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing