3GZS | pdb_00003gzs

Crystal structure of a susd superfamily protein (bf3413) from bacteroides fragilis nctc 9343 at 2.10 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.43	293	NANODROP, 25.0% PEG 3000, 0.1M Sodium acetate pH 4.43, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.921	α = 90
b = 50.377	β = 108.05
c = 117.95	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 325 mm CCD	Flat mirror, vertical and horizontal focusing mirrors	2009-01-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.91837, 0.97946, 0.97907	SSRL	BL12-2

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	2.09	29.63	93.2	0.041				57418		-3	37.054

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	2.09	2.16	77.9		0.403	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	2.09	29.63	57418	2934	97.27	0.158	0.156	0.17	0.198	0.21	RANDOM	51.818

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]
0.81		0.3	-0.43		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.557
r_dihedral_angle_4_deg	11.981
r_dihedral_angle_3_deg	10.288
r_scangle_it	5.217
r_scbond_it	4.052
r_dihedral_angle_1_deg	3.357
r_mcangle_it	2.283
r_mcbond_it	1.598
r_angle_refined_deg	1.157
r_angle_other_deg	0.983
r_mcbond_other	0.401
r_symmetry_hbond_refined	0.218
r_nbd_refined	0.201
r_symmetry_vdw_other	0.199
r_nbtor_refined	0.181
r_symmetry_vdw_refined	0.181
r_nbd_other	0.17
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.087
r_nbtor_other	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7734
Nucleic Acid Atoms
Solvent Atoms	503
Heterogen Atoms	64

Software

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