2PP7

Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	6-11% PEG 4000, 100mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.111	α = 90
b = 101.833	β = 90
c = 145.508	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	77	IMAGE PLATE	MARRESEARCH	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.65	30		0.086		6.2		111530

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.71			0.361		4.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.65	30	100105	5258	95.96	0.15499	0.15369	0.17951	RANDOM	19.813

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]
1.84			-0.09		-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.999
r_dihedral_angle_4_deg	19.461
r_dihedral_angle_3_deg	12.199
r_dihedral_angle_1_deg	6.875
r_scangle_it	2.948
r_scbond_it	1.921
r_angle_refined_deg	1.341
r_mcangle_it	1.104
r_mcbond_it	0.711
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.999
r_dihedral_angle_4_deg	19.461
r_dihedral_angle_3_deg	12.199
r_dihedral_angle_1_deg	6.875
r_scangle_it	2.948
r_scbond_it	1.921
r_angle_refined_deg	1.341
r_mcangle_it	1.104
r_mcbond_it	0.711
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.225
r_nbd_refined	0.194
r_symmetry_hbond_refined	0.126
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.093
r_metal_ion_refined	0.025
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7687
Nucleic Acid Atoms
Solvent Atoms	1021
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.