9PRB | pdb_00009prb

Crystal structure of the N-terminal domain of the A subunit of the Bacillus cereus GerI germinant receptor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	289	0.1 M HEPES, pH 7.), 1.8-2.0 M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.149	α = 90
b = 122.846	β = 90
c = 212.188	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER2 X 16M		2021-05-21	M	MAD
2	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 16M		2021-05-21	M	MAD
3	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2022-07-13	M	SINGLE WAVELENGTH
4	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2022-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97929	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9795	SSRL	BL9-2
3	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.9793	NSLS-II	17-ID-2
4	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.89	78.64	95.9	0.061	0.063	0.015	1	31.6	18.3		26911			35.12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.92	94		1.294	1.329	0.303	0.907	2.2	19

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	SAD	THROUGHOUT	2.8	38.3	26875	1996	99.9	0.201	0.199	0.1873	0.229	0.2182	RANDOM	87.84

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]
-2.2623			-26.3398		28.6021

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	3.66
t_omega_torsion	2.61
t_angle_deg	1.17
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5798
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	4

Software

Software
Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing