3BO9 | pdb_00003bo9

Crystal structure of putative nitroalkan dioxygenase (TM0800) from Thermotoga maritima at 2.71 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.67	293	NANODROP, 44.0% PEG 400, 0.2M Lithium sulfate, 0.1M Tris-HCl pH 8.67, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.63	73.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.058	α = 90
b = 128.058	β = 90
c = 161.678	γ = 90

Symmetry
Space Group	P 43 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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-10-27	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.91840, 0.97939, 0.97953	APS	23-ID-D

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	2.71	29.761	99.9	0.171	0.171	3.7	7.3		37210			67.24

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	2.71	2.78	100		1.555	1.555	0.4	7.4	2725

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	2.71	29.761	37145	1854	99.88	0.19	0.189	0.19	0.211	0.21	RANDOM	39.802

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]
-0.36			-0.36		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.217
r_dihedral_angle_4_deg	14.746
r_dihedral_angle_3_deg	13.241
r_scangle_it	6.594
r_scbond_it	4.57
r_dihedral_angle_1_deg	3.663
r_mcangle_it	2.192
r_mcbond_it	1.572
r_angle_refined_deg	1.312
r_angle_other_deg	0.894
r_mcbond_other	0.282
r_symmetry_vdw_other	0.223
r_nbd_refined	0.216
r_xyhbond_nbd_refined	0.189
r_nbd_other	0.188
r_nbtor_refined	0.177
r_symmetry_vdw_refined	0.142
r_symmetry_hbond_refined	0.096
r_nbtor_other	0.086
r_chiral_restr	0.073
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4663
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	152

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction