1XHC

NADH oxidase /nitrite reductase from Pyrococcus furiosus Pfu-1140779-001

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F3P	pdb entry 1F3P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	modified microbatch	3.8	315	14%w/v PEG-4000, 0.15M sodium chloride, 0.15M magnesium chloride, 0.1M sodium acetate, modified microbatch, temperature 315K, pH 3.8
2	modified microbatch	3.8	315	18%w/v PEG-4000, 0.15M sodium chloride, 0.15M magnesium chloride, 0.1M sodium acetate, modified microbatch, temperature 315K, pH 3.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.335	α = 90
b = 73.737	β = 90
c = 95.849	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID
2	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.15	20	92.2	0.112				22114

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.15	2.32	64.5		0.474

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 (All)	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	pdb entry 1F3P	2.35	58.722	18210	915	99.378	0.202	0.20202	0.2	0.22	0.2412	0.27	RANDOM	37.008

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]
0.689			0.965		-1.654

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.402
r_dihedral_angle_4_deg	20.027
r_dihedral_angle_3_deg	14.946
r_dihedral_angle_1_deg	6.553
r_scangle_it	2.457
r_scbond_it	1.558
r_angle_refined_deg	1.407
r_mcangle_it	1.062
r_scangle_other	0.921
r_angle_other_deg	0.793
r_mcbond_it	0.77
r_scbond_other	0.589
r_mcangle_other	0.511
r_symmetry_vdw_refined	0.308
r_symmetry_vdw_other	0.205
r_nbd_refined	0.189
r_nbtor_refined	0.172
r_nbd_other	0.169
r_symmetry_hbond_refined	0.161
r_xyhbond_nbd_refined	0.136
r_mcbond_other	0.127
r_chiral_restr	0.084
r_nbtor_other	0.08
r_xyhbond_nbd_other	0.031
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2637
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	53

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CNS	phasing