9RNZ | pdb_00009rnz

Atomic resolution (1.02 A) XFEL structure of nitrite-bound copper nitrite reductase from Bradyrhizobium sp. determined by serial femtosecond rotation crystallography (SF-ROX) at 100 K

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8RFL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	1.8 M ammonium sulphate, 100 mM Tris (pH 7.3)

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.89	α = 90
b = 103.89	β = 90
c = 64.35	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	RAYONIX MX300-HS		2022-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	0.954	SACLA	BL2

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	Single crystal (SF-ROX)	fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	Single crystal (SF-ROX)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	17	99.9	0.935	0.166	5.3	20		212451			8.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.01			0.206	0.986	1.2

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	1.02	16.765	200220	10169	99.97	0.147	0.1461	0.1463	0.1607	0.161	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	20.383
r_lrange_other	17.259
r_dihedral_angle_6_deg	15.983
r_dihedral_angle_2_deg	13.426
r_dihedral_angle_3_deg	13.16
r_mcangle_it	8.984
r_mcangle_other	8.982
r_dihedral_angle_1_deg	7.829
r_scangle_it	7.009
r_scangle_other	6.867
r_mcbond_it	6.197
r_mcbond_other	6.194
r_scbond_it	4.67
r_scbond_other	4.534
r_rigid_bond_restr	2.968
r_angle_refined_deg	1.615
r_angle_other_deg	0.658
r_symmetry_xyhbond_nbd_other	0.275
r_nbd_refined	0.246
r_xyhbond_nbd_refined	0.226
r_symmetry_nbd_other	0.193
r_symmetry_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.178
r_nbd_other	0.169
r_metal_ion_refined	0.132
r_symmetry_nbd_refined	0.125
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_symmetry_metal_ion_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2554
Nucleic Acid Atoms
Solvent Atoms	438
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASES	phasing