28PB | pdb_000028pb

Crystal structure of CbcA periplasmic domain from Geobacter sulfurreducens

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293.15	1.4 M trisodium citrate and 0.1 M sodium HEPES (pH 8)

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.436	α = 90
b = 94.167	β = 90
c = 114.175	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 EIGER2 X 9M		2023-07-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.873	ESRF	ID30B

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	1.91	94.17	100	0.199	0.207	0.056	0.991	9	13.7		58831

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	1.96	99.9		0.308		14.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.91	72.752	58760	2876	99.985	0.202	0.1991	0.1996	0.2531	0.2542	51.275

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]
-0.253			-0.43		0.684

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.96
r_dihedral_angle_6_deg	14.186
r_lrange_it	9.539
r_dihedral_angle_2_deg	8.005
r_dihedral_angle_1_deg	7.115
r_scangle_it	6.686
r_mcangle_it	5.668
r_scbond_it	4.412
r_mcbond_it	3.632
r_angle_refined_deg	2.177
r_nbtor_refined	0.302
r_nbd_refined	0.226
r_symmetry_nbd_refined	0.216
r_xyhbond_nbd_refined	0.2
r_symmetry_xyhbond_nbd_refined	0.155
r_metal_ion_refined	0.144
r_chiral_restr	0.113
r_bond_refined_d	0.015
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4256
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	605

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
AutoSol	phasing