7QFG | pdb_00007qfg

Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain III (aa 309-444)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7QEH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Index screen condition A9 (0.1 M BIS-TRIS pH 5.5, 3.0 M Sodium chloride) with protein end concentration of 10 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.628	α = 90
b = 43.943	β = 98.824
c = 42.488	γ = 90

Symmetry
Space Group	C 1 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 EIGER2 X 16M		2019-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.25430	PETRA III, DESY	P11

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	1.65	41.99	99.4	0.074	0.102	0.07	0.985	11.3	3.2		22102

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	1.65	1.68			0.15	0.206	0.141	0.951		3

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	7QEH	1.65	41.99	22101	1143	99.321	0.16	0.1585	0.17	0.1836	0.19	16.567

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]
0.134		-0.092	0.609		-0.682

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.61
r_dihedral_angle_3_deg	11.856
r_dihedral_angle_4_deg	9.205
r_dihedral_angle_1_deg	7.026
r_lrange_it	5.84
r_lrange_other	5.608
r_scangle_it	4.855
r_scangle_other	4.852
r_scbond_it	3.119
r_scbond_other	3.116
r_mcangle_other	2.284
r_mcangle_it	2.279
r_angle_refined_deg	1.908
r_mcbond_it	1.54
r_mcbond_other	1.49
r_angle_other_deg	1.457
r_nbd_refined	0.214
r_symmetry_xyhbond_nbd_refined	0.21
r_xyhbond_nbd_refined	0.206
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.175
r_nbd_other	0.16
r_symmetry_nbd_refined	0.151
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1081
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	18

Software

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