2R01 | pdb_00002r01

Crystal structure of a putative fmn-dependent nitroreductase (ct0345) from chlorobium tepidum tls at 1.15 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.7	277	NANODROP, 0.2M KH2PO4, 20.0% PEG 3350, No Buffer pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.03	α = 90
b = 64.72	β = 90
c = 48.01	γ = 90

Symmetry
Space Group	P 21 21 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 mirror (vertical focusing)	2007-07-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97949, 0.97922	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	1.15	28.49	98.8	0.045	10.2	3.14		66535			7.078

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)
	1.15	1.19	96.6		0.347	2.19

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 (All)	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	1.15	28.49	66493	3361	99.13	0.149	0.149	0.148	0.16	0.165	0.17	RANDOM	8.107

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]
-0.54			0.02		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.818
r_dihedral_angle_4_deg	9.522
r_dihedral_angle_3_deg	9.308
r_sphericity_free	5.387
r_dihedral_angle_1_deg	5.27
r_scangle_it	3.34
r_sphericity_bonded	2.608
r_scbond_it	2.392
r_mcangle_it	1.846
r_rigid_bond_restr	1.456
r_angle_refined_deg	1.454
r_mcbond_it	1.243
r_angle_other_deg	0.916
r_mcbond_other	0.478
r_symmetry_vdw_other	0.3
r_symmetry_vdw_refined	0.252
r_nbd_refined	0.222
r_nbd_other	0.199
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.173
r_symmetry_hbond_refined	0.164
r_nbtor_other	0.087
r_chiral_restr	0.069
r_bond_refined_d	0.01
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	1478
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHARP	phasing
SHELXD	phasing