3M5K | pdb_00003m5k

Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (BDI_1728) from Parabacteroides distasonis ATCC 8503 at 1.86 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.47	293	14.0000% polyethylene glycol 1000, 0.3000M sodium chloride, 0.1M Na/K phosphate pH 6.47, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.639	α = 90
b = 149.639	β = 90
c = 149.639	γ = 90

Symmetry
Space Group	P 43 3 2

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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-11-06	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97946,0.97932	SSRL	BL9-2

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	1.86	29.347	99.8	0.086	12.7	10.669		48462		-3	25.884

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)
	1.86	1.93	99.7		0.821	2.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.86	29.347	48417	2446	99.85	0.161	0.16	0.16	0.178	0.18	RANDOM	26.696

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.795
r_dihedral_angle_4_deg	14.534
r_dihedral_angle_3_deg	13.843
r_dihedral_angle_1_deg	5.292
r_scangle_it	4.653
r_scbond_it	3.383
r_mcangle_it	2.507
r_mcbond_it	1.951
r_angle_refined_deg	1.434
r_angle_other_deg	0.988
r_mcbond_other	0.563
r_symmetry_vdw_other	0.286
r_nbd_refined	0.224
r_nbd_other	0.206
r_symmetry_hbond_refined	0.183
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.17
r_symmetry_vdw_refined	0.166
r_chiral_restr	0.087
r_nbtor_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2676
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	79

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing