8RVM

Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in space group P63

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	293	17-20 % PEG 3350, 0.1 M Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.2	α = 90
b = 114.2	β = 90
c = 64.8	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	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	1.6	98.9	99.9	0.888	14.6	11.3		59330

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.74			0.656

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	THROUGHOUT	1.6	98.9	59330	2709	99.902	0.197	0.1942	0.2433	21.496

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]
-0.507	-0.254		-0.507		1.646

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.6
r_dihedral_angle_3_deg	15.556
r_dihedral_angle_4_deg	14.312
r_dihedral_angle_other_3_deg	11.739
r_dihedral_angle_1_deg	7.297
r_lrange_it	4.675
r_lrange_other	4.597
r_scangle_it	3.137
r_scangle_other	3.134
r_angle_refined_deg	2.794
r_mcangle_it	2.683
r_mcangle_other	2.683
r_scbond_it	2.079
r_scbond_other	2.077
r_mcbond_it	1.849
r_mcbond_other	1.841
r_angle_other_deg	1.553
r_nbd_refined	0.203
r_symmetry_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.166
r_chiral_restr	0.161
r_symmetry_nbd_refined	0.158
r_xyhbond_nbd_refined	0.147
r_nbd_other	0.139
r_symmetry_xyhbond_nbd_other	0.133
r_metal_ion_refined	0.095
r_symmetry_nbtor_other	0.093
r_gen_planes_other	0.016
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3891
Nucleic Acid Atoms
Solvent Atoms	505
Heterogen Atoms	350

Software

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