9HB9 | pdb_00009hb9

A. vinelandii nitrogenase MoFe protein Anc1a

X-RAY DIFFRACTION

---

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	0.2 M LiSO4 x 1 H2O, 0.1 M bis-Tris/HCl at pH 6.5, 25%(w/v) of polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.29	α = 90
b = 138.615	β = 90
c = 208.581	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 CdTe 16M		2023-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.638	19.879	93.7	0.368	0.106	0.989	7.1	12.8		46401

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.658	2.912	51.8		0.425

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.658	19.879	46401	2377	77.828	0.172	0.169	0.1725	0.2202	0.2168	41.992

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]
0.251			-0.279		0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.777
r_dihedral_angle_6_deg	13.877
r_dihedral_angle_other_3_deg	9.007
r_dihedral_angle_1_deg	6.368
r_lrange_it	6.265
r_lrange_other	6.264
r_dihedral_angle_2_deg	4.4
r_scangle_it	4.328
r_scangle_other	4.327
r_mcangle_it	3.523
r_mcangle_other	3.523
r_scbond_it	2.579
r_scbond_other	2.579
r_mcbond_it	2.161
r_mcbond_other	2.161
r_angle_refined_deg	1.267
r_angle_other_deg	0.454
r_nbd_refined	0.207
r_nbd_other	0.205
r_symmetry_nbd_refined	0.204
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.153
r_xyhbond_nbd_refined	0.149
r_metal_ion_refined	0.123
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_1	0.076
r_ncsr_local_group_2	0.067
r_chiral_restr	0.061
r_bond_refined_d	0.021
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15942
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	96

Software

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