4D4B

The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with MSMSMe

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
2.21	44.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.55	α = 90
b = 85.226	β = 90
c = 102.003	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		2014-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

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	1.3	43.8	100	0.06	21.5	12.8		178799		-3.7	15.6

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	1.3	1.32	99.9		1.22	2.3	10.4

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	1.3	65.4	170002	8695	99.99	0.12247	0.12097	0.15161	RANDOM	22.501

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]
0.03			-0.09		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.601
r_sphericity_free	36.348
r_dihedral_angle_4_deg	25.646
r_sphericity_bonded	12.137
r_dihedral_angle_3_deg	11.548
r_dihedral_angle_1_deg	5.679
r_scangle_it	3.142
r_scbond_it	2.761
r_rigid_bond_restr	2.535
r_mcangle_it	2.462
r_mcbond_it	2.048
r_mcbond_other	2.048
r_angle_refined_deg	1.386
r_angle_other_deg	0.86
r_symmetry_vdw_refined	0.358
r_symmetry_vdw_other	0.321
r_nbd_refined	0.269
r_symmetry_hbond_refined	0.237
r_nbtor_refined	0.19
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.125
r_xyhbond_nbd_other	0.118
r_chiral_restr	0.088
r_nbtor_other	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_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	5382
Nucleic Acid Atoms
Solvent Atoms	1035
Heterogen Atoms	56

Software

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