9F8X

Low-dose structure of Marinobacter nauticus nitrous oxide reductase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QNI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	303	15 % PEG 8000 0.6 M NaCl 0.1 M imidazole/malate protein concentration: 14 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.26	α = 81.384
b = 69.375	β = 77.918
c = 153.188	γ = 88.608

Symmetry
Space Group	P 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	IMAGE PLATE	MAR scanner 345 mm plate	Varimax HF	2020-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.498	23.501	91.4	0.026	0.026	1	12.1	2		381570	2		13.5

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	1.498	1.52	83.4		0.258	0.258	0.87	3	1.9

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.498	23.501	381568	19047	91.341	0.131	0.1298	0.1519	16.34

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]
-0.832	0.006	0.534	0.854	-0.079	0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.107
r_dihedral_angle_3_deg	13.613
r_dihedral_angle_2_deg	8.049
r_dihedral_angle_1_deg	7.606
r_lrange_it	5.661
r_lrange_other	5.66
r_scangle_it	3.854
r_scangle_other	3.854
r_scbond_it	2.58
r_scbond_other	2.58
r_angle_refined_deg	2.075
r_mcangle_other	1.742
r_mcangle_it	1.741
r_mcbond_it	1.233
r_mcbond_other	1.233
r_angle_other_deg	0.606
r_symmetry_xyhbond_nbd_refined	0.226
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.194
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.175
r_nbd_other	0.175
r_symmetry_nbd_refined	0.174
r_chiral_restr	0.112
r_metal_ion_refined	0.112
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.076
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18072
Nucleic Acid Atoms
Solvent Atoms	3222
Heterogen Atoms	99

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
Aimless	data scaling
MOLREP	phasing