3GFA

Crystal structure of a putative nitroreductase in complex with fmn (cd3205) from clostridium difficile 630 at 1.35 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.7	277	43.1000% 2-methyl-2,4-pentanediol, 0.1M phosphate-citrate pH 3.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.336	α = 90
b = 109.891	β = 104.84
c = 60.635	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)	2008-11-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91162,0.97831,0.97870	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.35	29.988	98.2	0.082	0.082	3.938	3.7		99649			14.166

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.39	81.9		0.496	0.496	1.5	3	6124

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	1.35	29.988	99648	4983	98.22	0.135	0.134	0.157	RANDOM	18.461

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]
-0.4		-0.96	-0.38		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.42
r_dihedral_angle_4_deg	13.771
r_dihedral_angle_3_deg	12.78
r_sphericity_free	7.409
r_dihedral_angle_1_deg	5.547
r_sphericity_bonded	3.701
r_scangle_it	2.876
r_mcangle_it	2.61
r_scbond_it	2.093
r_mcbond_it	1.932
r_angle_refined_deg	1.504
r_rigid_bond_restr	1.335
r_mcbond_other	1.026
r_angle_other_deg	0.941
r_symmetry_vdw_refined	0.267
r_symmetry_vdw_other	0.225
r_nbd_refined	0.223
r_symmetry_hbond_refined	0.205
r_nbd_other	0.201
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.15
r_nbtor_other	0.089
r_chiral_restr	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3077
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms	98

Software

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