2RAF | pdb_00002raf

Crystal structure of putative dinucleotide-binding oxidoreductase (NP_786167.1) from Lactobacillus plantarum at 1.60 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	NANODROP, 20.0% PEG 3350, 0.2M Ammonium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.33	α = 90
b = 152.57	β = 90
c = 140.07	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-07-25	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97886, 0.97917	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	1.6	29.54	99.2	0.053	10.8			75349		-3	20.872

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)
	1.6	1.66	98.5		0.368	2.2

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	1.6	29.54	75306	3791	99.59	0.153	0.151	0.16	0.186	0.19	RANDOM	11.56

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]
0.29			-0.14		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.163
r_dihedral_angle_3_deg	10.461
r_dihedral_angle_4_deg	7.544
r_scangle_it	6.387
r_dihedral_angle_1_deg	4.599
r_scbond_it	4.512
r_mcangle_it	2.789
r_mcbond_it	2.227
r_angle_refined_deg	1.751
r_angle_other_deg	1.42
r_mcbond_other	0.532
r_symmetry_vdw_other	0.239
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.198
r_nbtor_refined	0.175
r_symmetry_hbond_refined	0.175
r_nbd_other	0.157
r_xyhbond_nbd_refined	0.157
r_xyhbond_nbd_other	0.134
r_chiral_restr	0.086
r_nbtor_other	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4543
Nucleic Acid Atoms
Solvent Atoms	626
Heterogen Atoms	48

Software

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