9HBN | pdb_00009hbn

A. vinelandii nitrogenase MoFe protein Anc1b

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		293	0.1 M MES/imidazole at pH 6.5, 12.5% of (w/v) of polyethylene glycol 1000, 3350 and (v/v) 2-methyl-2,4-pentandiol each and 0.02 M of 1,6-hexanediol, 1-butanol, 1,4-butanediol, (RS)-1,2-propanediol, 2-propanol, and 1,3-propanediol, each

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.083	α = 90
b = 128.984	β = 90
c = 209.445	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 EIGER2 X 9M		2023-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8856	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.824	109.828	94.4	0.068	0.997	7.5	13.1		91363

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	1.824	2.105			1.419	0.401	0.727

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	1.824	109.828	91363	4516	49.109	0.209	0.2063	0.2145	0.2686	0.2745	RANDOM	24.338

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]
-1.3			-0.365		1.665

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.874
r_dihedral_angle_6_deg	14.799
r_dihedral_angle_1_deg	7.261
r_dihedral_angle_2_deg	6.919
r_lrange_it	3.97
r_lrange_other	3.917
r_scangle_it	2.291
r_scangle_other	2.291
r_angle_refined_deg	1.698
r_mcangle_it	1.598
r_mcangle_other	1.598
r_scbond_it	1.354
r_scbond_other	1.354
r_mcbond_it	0.955
r_mcbond_other	0.955
r_angle_other_deg	0.583
r_nbd_other	0.25
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.208
r_xyhbond_nbd_refined	0.207
r_symmetry_nbd_other	0.203
r_symmetry_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.183
r_chiral_restr	0.115
r_metal_ion_refined	0.108
r_symmetry_xyhbond_nbd_other	0.091
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15974
Nucleic Acid Atoms
Solvent Atoms	689
Heterogen Atoms	112

Software

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