3E39 | pdb_00003e39

Crystal structure of a putative nitroreductase in complex with fmn (dde_0787) from desulfovibrio desulfuricans subsp. at 1.70 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% PEG-400, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.78	α = 90
b = 67.99	β = 90
c = 99.74	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 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	0.918370,0.979421,0.979155	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	1.7	28.094	96.9	0.078	8.85			36111		-3	13.566

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)
	1.7	1.76	99		0.461	1.8

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	1.7	28.094	36077	1806	98.96	0.166	0.165	0.17	0.201	0.2	RANDOM	10.969

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]
0.59			0.34		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.633
r_dihedral_angle_3_deg	10.441
r_dihedral_angle_4_deg	10.254
r_scangle_it	5.229
r_dihedral_angle_1_deg	4.117
r_scbond_it	3.766
r_mcangle_it	2.44
r_mcbond_it	1.856
r_angle_refined_deg	1.524
r_angle_other_deg	0.983
r_mcbond_other	0.478
r_symmetry_vdw_other	0.284
r_nbd_refined	0.221
r_nbd_other	0.216
r_nbtor_refined	0.176
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.157
r_symmetry_vdw_refined	0.127
r_chiral_restr	0.097
r_nbtor_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2664
Nucleic Acid Atoms
Solvent Atoms	373
Heterogen Atoms	84

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