9FUH | pdb_00009fuh

CRYSTAL STRUCTURE OF REDUCED WILD TYPE THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZIY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	277	100 mM bis-tris propane pH 7.7, 200 mM sodium citrate, and 22% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.842	α = 90
b = 127.842	β = 90
c = 86.337	γ = 120

Symmetry
Space Group	H 3

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 EIGER X 16M		2021-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.87000	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.17	37.685	100	0.089	0.099	0.044	0.998	7.9	4.9		177553			9.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.17	1.19	100		1.642	1.846	0.836	0.354	0.9	4.8

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	FOURIER SYNTHESIS	THROUGHOUT	1.17	37.685	177460	8797	99.944	0.123	0.1217	0.1217	0.1461	0.1462	RANDOM	16.971

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]
0.118	0.059		0.118		-0.384

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.016
r_dihedral_angle_6_deg	16.202
r_lrange_other	15.712
r_dihedral_angle_3_deg	11.725
r_scangle_it	8.583
r_scangle_other	8.577
r_dihedral_angle_2_deg	8.068
r_dihedral_angle_1_deg	7.016
r_scbond_it	6.157
r_scbond_other	6.148
r_mcangle_other	5.216
r_mcangle_it	5.209
r_rigid_bond_restr	3.963
r_mcbond_it	3.838
r_mcbond_other	3.816
r_angle_refined_deg	1.883
r_angle_other_deg	0.69
r_symmetry_nbd_refined	0.263
r_xyhbond_nbd_refined	0.245
r_nbd_refined	0.24
r_symmetry_xyhbond_nbd_refined	0.219
r_symmetry_xyhbond_nbd_other	0.212
r_nbd_other	0.206
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.18
r_chiral_restr	0.118
r_symmetry_nbtor_other	0.087
r_symmetry_metal_ion_refined	0.038
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_xyhbond_nbd_other	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3423
Nucleic Acid Atoms
Solvent Atoms	711
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
Coot	model building
REFMAC	phasing