9OVI | pdb_00009ovi

Crystal Structure of SH3-like_bac-type domain (79-145) of Conserved domain protein GBAA_2967 from Bacillus anthracis Ames ancestor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A0A6L7HMQ8-F1	UniProt

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	292	Protein: 6.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: JCSG+ (A5), 0.2M Magnesium formate, 20% (w/v) PEG3350; Cryo: Reservoir

Crystal Properties
Matthews coefficient	Solvent content
2.6	51.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.281	α = 90
b = 50.276	β = 90
c = 84.602	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	CCD	MARMOSAIC 225 mm CCD		2013-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.5	30	99.4	0.075	0.075	0.081	0.03	0.997	24.1	7		25567		-3	14.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	91.3		0.859	0.859	0.949	0.394	0.714	2.1	5.5

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.5	29.42	24144	1319	99.83	0.16548	0.16448	0.1656	0.18385	0.1854	RANDOM	16.069

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]
0.6			-1.11		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	8.022
r_long_range_B_refined	7.059
r_long_range_B_other	6.608
r_dihedral_angle_1_deg	5.99
r_scangle_other	3.297
r_scbond_it	2.128
r_scbond_other	2.095
r_dihedral_angle_2_deg	1.854
r_mcangle_it	1.771
r_mcangle_other	1.77
r_angle_refined_deg	1.203
r_mcbond_it	1.05
r_mcbond_other	1.049
r_angle_other_deg	0.456
r_chiral_restr	0.073
r_gen_planes_refined	0.015
r_gen_planes_other	0.012
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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	1082
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing