8BT9 | pdb_00008bt9

Crystal structure of SlpA domain II (aa 201-310), domain that is involved in the self-assembly and dimerization of the S-layer from Lactobacillus acidophilus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Condition: 1.0 M Sodium citrate tribasic dihydrate, 0.1 M MES, pH 6.5 Protein: 10 mg/ml in 150 mM NaCl, 25 mM HEPES, pH 7.0 0.5 ul protein mixed with 0.5 ul condition

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.69	α = 90
b = 137.69	β = 90
c = 51.301	γ = 120

Symmetry
Space Group	P 32 2 1

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 EIGER X 16M		2022-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033230	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	47.124	99.97	0.01155	1	23.76	2		32853			56.71

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.175	99.97		0.4849	0.909	1.57	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	MOLECULAR REPLACEMENT	FREE R-VALUE	2.1	47.124	32853	1696	99.976	0.191	0.1892	0.2	0.2221	0.23	69.669

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]
-0.753	-0.376		-0.753		2.442

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.309
r_dihedral_angle_3_deg	13.926
r_lrange_it	10.821
r_lrange_other	10.806
r_scangle_it	8.016
r_scangle_other	8.014
r_dihedral_angle_1_deg	7.587
r_mcangle_it	6.654
r_mcangle_other	6.652
r_dihedral_angle_2_deg	5.864
r_scbond_it	5.68
r_scbond_other	5.678
r_mcbond_it	4.806
r_mcbond_other	4.804
r_angle_refined_deg	1.498
r_angle_other_deg	0.518
r_nbd_refined	0.223
r_symmetry_nbd_refined	0.215
r_xyhbond_nbd_refined	0.212
r_nbd_other	0.206
r_symmetry_nbd_other	0.188
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.17
r_ncsr_local_group_3	0.135
r_ncsr_local_group_2	0.131
r_ncsr_local_group_1	0.125
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2495
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	9

Software

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