5AGD

An inactive (D125N) variant of the catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with alpha-1,6-mannopentaose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		PREVIOUSLY SOLVED NATIVE APO STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.1 M AMMONIUM NITRATE, PH 6.5, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.52	α = 90
b = 85.725	β = 90
c = 102.613	γ = 90

Symmetry
Space Group	P 21 21 21

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	DECTRIS PILATUS 6M		2014-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	1.2	44.02	99.5	0.04	18.6	7.9		228606		-3.7

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	1.2	1.22	94.2		1	1.9	7.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PREVIOUSLY SOLVED NATIVE APO STRUCTURE	1.2	65.79	217369	11136	99.42	0.12169	0.12054	0.14417	RANDOM	22.036

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]
0.28			-0.34		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.895
r_dihedral_angle_2_deg	38.487
r_dihedral_angle_4_deg	24.324
r_sphericity_bonded	13.026
r_dihedral_angle_3_deg	11.031
r_dihedral_angle_1_deg	5.292
r_rigid_bond_restr	2.754
r_scangle_it	2.622
r_scbond_it	2.264
r_mcangle_it	2.005
r_mcbond_it	1.719
r_mcbond_other	1.716
r_angle_refined_deg	1.436
r_angle_other_deg	1.147
r_symmetry_hbond_refined	0.465
r_symmetry_hbond_other	0.283
r_symmetry_vdw_refined	0.281
r_symmetry_vdw_other	0.265
r_nbd_refined	0.261
r_nbtor_refined	0.19
r_nbd_other	0.187
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.104
r_nbtor_other	0.075
r_xyhbond_nbd_other	0.049
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5372
Nucleic Acid Atoms
Solvent Atoms	1032
Heterogen Atoms	136

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing