7QFI | pdb_00007qfi

Crystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain I (aa 31-182)

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 15 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; SG+ screen condition 50 (25 % w/v PEG 3350) with protein end concentration of 7.5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.35	α = 90
b = 38.347	β = 93.927
c = 82.745	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 2M		2018-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

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	1.5	41.28	99.1	0.073	0.101	0.069	0.995	7.7	3.2		37359

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	1.5	1.53			0.479	0.653	0.441	0.755		2.9

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	AB INITIO PHASING	FREE R-VALUE	1.5	41.28	37340	1877	98.914	0.188	0.1868	0.19	0.2224	0.22	19.25

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]
1.353		-0.57	1.006		-2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.448
r_dihedral_angle_4_deg	31.783
r_dihedral_angle_3_deg	11.99
r_dihedral_angle_1_deg	7.545
r_lrange_it	6.574
r_lrange_other	6.481
r_scangle_it	4.767
r_scangle_other	4.766
r_scbond_it	3.095
r_scbond_other	3.094
r_mcangle_it	2.904
r_mcangle_other	2.878
r_mcbond_it	1.992
r_mcbond_other	1.958
r_angle_refined_deg	1.726
r_angle_other_deg	1.512
r_symmetry_nbd_refined	0.247
r_nbd_other	0.237
r_symmetry_xyhbond_nbd_refined	0.21
r_nbd_refined	0.192
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.157
r_ncsr_local_group_1	0.154
r_xyhbond_nbd_other	0.085
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.07
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1949
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Arcimboldo	phasing
ARP/wARP	model building