3JR7 | pdb_00003jr7

The crystal structure of the protein of DegV family COG1307 with unknown function from Ruminococcus gnavus ATCC 29149

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	289	0.2M Sodium chloride, 0.1M Phosphate-citrate, 10%PEG3000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.899	α = 90
b = 96.899	β = 90
c = 159.921	γ = 120

Symmetry
Space Group	P 31 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	SBC-3	mirrors	2008-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9794	APS	19-BM

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	2	83.92	99.41	0.077	17.85	5.2	56152	55821	2	2

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	2	2.055	99.52		0.352	2.1	4.5	4365

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2	83.92	56152	55821	2970	99.41	0.16432	0.16198	0.1756	0.20843	0.2122	RANDOM	22.259

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]
0.58	0.29		0.58		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.58
r_dihedral_angle_4_deg	18.996
r_dihedral_angle_3_deg	13.833
r_sphericity_free	7.259
r_dihedral_angle_1_deg	6.239
r_scangle_it	5.628
r_scbond_it	3.665
r_sphericity_bonded	2.874
r_mcangle_it	2.24
r_rigid_bond_restr	1.868
r_angle_refined_deg	1.673
r_mcbond_it	1.331
r_angle_other_deg	0.914
r_mcbond_other	0.484
r_chiral_restr	0.091
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4294
Nucleic Acid Atoms
Solvent Atoms	545
Heterogen Atoms	50

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling