3FMB | pdb_00003fmb

Crystal structure of dimeric protein of unknown function and ferredoxin-like fold (YP_212648.1) from Bacteroides fragilis NCTC 9343 at 1.85 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	NANODROP, 0.2M (NH4)2SO4, 20.0% PEG 3350, No Buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.31	α = 90
b = 72.31	β = 90
c = 233.02	γ = 120

Symmetry
Space Group	P 61 2 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)	2008-11-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97867	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	1.85	29.399	99.7	0.09				31933		-3	29.156

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	1.85	1.92	98.6		0.012	1.7

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	1.85	29.399	31830	1612	99.72	0.172	0.17	0.17	0.205	0.2	RANDOM	32.402

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	31.697
r_dihedral_angle_4_deg	14.104
r_dihedral_angle_3_deg	13.028
r_scangle_it	6.465
r_dihedral_angle_1_deg	5.545
r_scbond_it	4.731
r_mcangle_it	2.44
r_mcbond_it	2.08
r_angle_refined_deg	1.468
r_angle_other_deg	0.971
r_mcbond_other	0.508
r_nbd_refined	0.212
r_nbd_other	0.199
r_symmetry_hbond_refined	0.186
r_symmetry_vdw_other	0.185
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.167
r_symmetry_vdw_refined	0.148
r_chiral_restr	0.093
r_nbtor_other	0.085
r_bond_refined_d	0.017
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1646
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	30

Software

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