4MI6

Crystal structure of Gpb in complex with SUGAR (N-[4-(5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)BUTANOYL]-BETA-D-GLUCOPYRANOSYLAMINE)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SYM	pdb entry 3SYM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	289	10mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.9	α = 90
b = 128.9	β = 90
c = 116.54	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	MAR CCD 165 mm		2013-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.04	MAX II	I911-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	23.94	98.1	0.055	13.2	3.4	75897	75897		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	97.1		0.365	3.2	3.4	10836

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 3SYM	1.9	23.71	72040	72040	3821	97.78	0.16265	0.16131	0.1885	RANDOM	31.341

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]
0.71			0.71		-1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.316
r_dihedral_angle_4_deg	18.972
r_dihedral_angle_3_deg	15.05
r_dihedral_angle_1_deg	5.812
r_long_range_B_refined	5.182
r_long_range_B_other	5.182
r_scangle_other	3.577
r_mcangle_it	2.461
r_mcangle_other	2.461
r_scbond_it	2.119
r_scbond_other	2.119
r_mcbond_it	1.52
r_mcbond_other	1.52
r_angle_refined_deg	1.186
r_angle_other_deg	0.804
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6601
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	27

Software

Software
Software Name	Purpose
MAR345	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing