8RXU | pdb_00008rxu

Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in space group P21

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UU9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	278	17-20 % PEG 3350, 0.1 M Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.2	α = 90
b = 64.8	β = 119.9
c = 114.2	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 12M		2018-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97242	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.737	42.877	98	0.996	10.7	4.2		145919

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.737	1.83			0.956	0.844

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.737	42.877	145919	7348	97.76	0.195	0.1913	0.2	0.2542	0.26	21.354

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]
-2.737		5.607	9.76		-7.023

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.525
r_dihedral_angle_3_deg	19.199
r_dihedral_angle_4_deg	16.883
r_dihedral_angle_other_3_deg	12.447
r_dihedral_angle_1_deg	8.494
r_lrange_it	3.976
r_lrange_other	3.951
r_angle_refined_deg	3.056
r_mcangle_it	2.893
r_mcangle_other	2.893
r_scangle_it	2.603
r_scangle_other	2.601
r_mcbond_it	2.181
r_mcbond_other	2.181
r_scbond_it	1.97
r_scbond_other	1.969
r_angle_other_deg	1.445
r_symmetry_xyhbond_nbd_refined	0.218
r_xyhbond_nbd_refined	0.215
r_nbd_refined	0.213
r_nbd_other	0.212
r_symmetry_nbd_other	0.204
r_symmetry_nbd_refined	0.198
r_chiral_restr	0.172
r_nbtor_refined	0.169
r_metal_ion_refined	0.126
r_symmetry_xyhbond_nbd_other	0.098
r_symmetry_nbtor_other	0.096
r_bond_refined_d	0.016
r_gen_planes_refined	0.015
r_gen_planes_other	0.015
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11665
Nucleic Acid Atoms
Solvent Atoms	950
Heterogen Atoms	1050

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing