9FUI | pdb_00009fui

CRYSTAL STRUCTURE OF NITRIC OXIDE TREATED F295L MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII

X-RAY DIFFRACTION

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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% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.275	α = 90
b = 128.275	β = 90
c = 86.348	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		2019-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.86999	Diamond	I03

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	37.057	97.2	0.063	0.07	0.032	0.999	10.3	4.7		173732

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	73.2		0.853	1.043	0.588	0.504	1	2.8

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	37.057	173704	8589	97.174	0.106	0.1052	0.1052	0.1274	0.1274	RANDOM	16.042

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]
0.111	0.056		0.111		-0.362

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.226
r_dihedral_angle_6_deg	16.125
r_lrange_other	13.622
r_dihedral_angle_3_deg	11.142
r_dihedral_angle_2_deg	8.199
r_dihedral_angle_1_deg	7.02
r_scangle_it	6.684
r_scangle_other	6.684
r_mcangle_other	4.772
r_mcangle_it	4.771
r_scbond_other	4.735
r_scbond_it	4.734
r_mcbond_it	3.394
r_rigid_bond_restr	3.369
r_mcbond_other	3.364
r_angle_refined_deg	1.804
r_angle_other_deg	0.68
r_symmetry_xyhbond_nbd_refined	0.271
r_nbd_refined	0.259
r_nbd_other	0.216
r_symmetry_nbd_refined	0.215
r_xyhbond_nbd_refined	0.212
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.175
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.085
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_gen_planes_other	0.007
r_metal_ion_refined	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3437
Nucleic Acid Atoms
Solvent Atoms	775
Heterogen Atoms	53

Software

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