8AOL | pdb_00008aol

Crystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain III (aa 363-499)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Wizard 1/2 screen condition 66 (20 % w/v PEG 3000, 200 mM Ca(OAc)2, 100 mM Tris base/HCl pH 7.0) with protein end concentration of 5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop

Crystal Properties
Matthews coefficient	Solvent content
5.3	76.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.174	α = 90
b = 133.174	β = 90
c = 70.572	γ = 120

Symmetry
Space Group	P 62 2 2

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		2018-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0332	ESRF	ID23-1

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	2.4	48.432	100	0.198	0.209	0.065	0.997	10.1	19.1		14935

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	2.4	2.49			1.516	1.596	0.496	0.844		19.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8ALU	2.4	48.432	14914	766	99.966	0.179	0.1779	0.19	0.205	0.21	46.79

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]
-3.069	-1.534		-3.069		9.955

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.375
r_lrange_it	16.475
r_lrange_other	16.469
r_dihedral_angle_4_deg	14.794
r_dihedral_angle_3_deg	14.677
r_scangle_it	13.869
r_scangle_other	13.862
r_scbond_it	11.134
r_scbond_other	11.125
r_dihedral_angle_1_deg	8.658
r_mcangle_other	5.21
r_mcangle_it	5.181
r_mcbond_it	3.748
r_mcbond_other	3.615
r_angle_refined_deg	1.777
r_angle_other_deg	1.33
r_symmetry_nbd_refined	0.238
r_xyhbond_nbd_refined	0.222
r_nbd_other	0.212
r_symmetry_metal_ion_refined	0.212
r_nbd_refined	0.189
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_other	0.167
r_symmetry_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.073
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1143
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	29

Software

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