2O34

Crystal structure of protein DVU1097 from Desulfovibrio vulgaris Hildenborough, Pfam DUF375

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6	295	2.0M sodium formate, 0.1M Na acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 4.60

Crystal Properties
Matthews coefficient	Solvent content
3.62	66.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.48	α = 90
b = 81.48	β = 90
c = 151.17	γ = 90

Symmetry
Space Group	P 21 21 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	MAR CCD 165 mm	SGX-CAT	2006-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID		APS	31-ID

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	1.98	50	96.3	0.106	8.3	4.8		55000

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)
	1.98	2.07	63.5		0.674		3.1

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	SAD	THROUGHOUT	1.95	19.98	31401	1717		0.213	0.21	0.21	0.273	0.28	RANDOM	49.78

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]
			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.64
r_dihedral_angle_3_deg	18.03
r_dihedral_angle_4_deg	17.905
r_dihedral_angle_1_deg	6.598
r_scangle_it	3.949
r_scbond_it	2.285
r_mcangle_it	1.791
r_angle_refined_deg	1.483
r_mcbond_it	0.966
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.225
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.167
r_metal_ion_refined	0.114
r_chiral_restr	0.106
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3566
Nucleic Acid Atoms
Solvent Atoms	374
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
SHELX	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXD	phasing