6FJA | pdb_00006fja

Crystal structure of T2D 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	7.5	298	Bis-Tris propane, 01M citrate, 22% P3350 MME

Crystal Properties
Matthews coefficient	Solvent content
2.75	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.23	α = 90
b = 128.23	β = 90
c = 86.11	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 PILATUS 6M	mirrors	2012-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.98	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (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	2.2	46.66	98.9	0.102	0.067	0.993	3.3		26499			40.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.26	90.9		0.535	0.43	0.559	2.1	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	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	3ZIY	2.2	46.66	25151	1343	98.88	0.13807	0.13608	0.14	0.17538	0.18	RANDOM	30.748

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]
-0.38	-0.19		-0.38		1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.368
r_dihedral_angle_4_deg	17.364
r_dihedral_angle_3_deg	14.093
r_long_range_B_refined	7.628
r_long_range_B_other	7.275
r_dihedral_angle_1_deg	6.736
r_scangle_other	4.338
r_scbond_other	2.636
r_scbond_it	2.635
r_mcangle_it	2.195
r_mcangle_other	2.195
r_angle_refined_deg	1.516
r_mcbond_it	1.457
r_mcbond_other	1.457
r_angle_other_deg	0.933
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3427
Nucleic Acid Atoms
Solvent Atoms	437
Heterogen Atoms	44

Software

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