3EO7 | pdb_00003eo7

Crystal structure of a putative nitroreductase (ava_2154) from anabaena variabilis atcc 29413 at 1.80 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	40.0000% 1,2-propanediol, 0.0500M Ca(OAc)2, 0.1M Acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.88	α = 90
b = 93.88	β = 90
c = 144.95	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	ADSC QUANTUM 315	Vertical focusing mirror	2008-07-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.918370,0.978985,0.979346	SSRL	BL9-1

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	1.8	30.056	99.6	0.068	14.56	7.3		68777		-3	20.106

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	1.8	1.86	97.9		0.618	2.3

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	1.8	30.056	68745	3480	99.72	0.138	0.137	0.14	0.163	0.17	RANDOM	23.88

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]
0.28	0.14		0.28		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.469
r_dihedral_angle_4_deg	13.228
r_dihedral_angle_3_deg	11.147
r_scangle_it	5.846
r_dihedral_angle_1_deg	4.328
r_scbond_it	4.239
r_mcangle_it	2.86
r_mcbond_it	2.003
r_angle_refined_deg	1.579
r_angle_other_deg	0.967
r_mcbond_other	0.474
r_symmetry_vdw_other	0.249
r_nbd_refined	0.222
r_nbd_other	0.205
r_metal_ion_refined	0.192
r_nbtor_refined	0.185
r_symmetry_hbond_refined	0.177
r_symmetry_vdw_refined	0.167
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.103
r_nbtor_other	0.086
r_bond_refined_d	0.014
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	3899
Nucleic Acid Atoms
Solvent Atoms	508
Heterogen Atoms	92

Software

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