4QSD | pdb_00004qsd

Crystal structure of atu4361 sugar transporter from Agrobacterium Fabrum C58, target efi-510558, with bound sucrose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4QSC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5		2.09 CRYSTALLIZATION CONDITIONS, PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 5% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100 RATIO); RESERVOIR: 0.1M TRIS-HCL, PH 8.5, 30% PEG400; CRYOPROTECTION: RESERVOIR PLUS 200MM SUCROSE; VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.025	α = 90
b = 76.564	β = 90.21
c = 67.873	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	PIXEL	PSI PILATUS 6M	MIRRORS	2014-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.34	50	97.9	0.037	0.037	13.2	4.3		80477		-5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.34	1.36	52.2		0.46	0.46	2.8	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	4QSC	1.34	50	78001	2317	97.7	0.122	0.121	0.14	0.151	0.17	RANDOM	23.13

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]
-0.48		0.05	0.04		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.958
r_sphericity_free	23.17
r_dihedral_angle_4_deg	18.461
r_dihedral_angle_3_deg	14.179
r_sphericity_bonded	10.732
r_rigid_bond_restr	6.122
r_dihedral_angle_1_deg	6.056
r_scbond_it	4.347
r_scbond_other	4.347
r_long_range_B_refined	4.142
r_long_range_B_other	4.142
r_scangle_other	3.99
r_mcangle_other	2.564
r_mcangle_it	2.553
r_mcbond_it	2.498
r_mcbond_other	2.484
r_angle_refined_deg	1.936
r_angle_other_deg	1.044
r_chiral_restr	0.195
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2965
Nucleic Acid Atoms
Solvent Atoms	491
Heterogen Atoms	69

Software

Software
Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing