3H4O

Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile 630 at 1.50 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	35.0000% Dioxane, 0.001 M flavin mononucleotide (FMN), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.897	α = 90
b = 63.487	β = 131.11
c = 55.465	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-02-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97840,0.97883	SSRL	BL11-1

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	1.5	29.348	96.6	0.052	9.97	3		32401		-3	12.217

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)
	1.5	1.55	90.9		0.388	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.5	29.348	32400	1637	99.47	0.141	0.139	0.167	RANDOM	15.258

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]
-0.39		-0.7	0.05		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.17
r_dihedral_angle_3_deg	12.883
r_dihedral_angle_4_deg	10.705
r_scangle_it	6.186
r_dihedral_angle_1_deg	5.764
r_scbond_it	4.034
r_mcangle_it	2.437
r_mcbond_it	1.865
r_angle_refined_deg	1.54
r_angle_other_deg	0.959
r_mcbond_other	0.425
r_symmetry_vdw_other	0.255
r_symmetry_vdw_refined	0.23
r_nbd_refined	0.216
r_nbd_other	0.202
r_nbtor_refined	0.176
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.145
r_nbtor_other	0.088
r_chiral_restr	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1381
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	47

Software

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