8W5B | pdb_00008w5b

Crystal Structure of the shaft pilin LrpA from Ligilactobacillus ruminis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8KB2	Crystal Structure of M- and C- Domains of the shaft pilin LrpA from Ligilactobacillus ruminis- iodide derivative
in silico model	AlphaFold		N-Domain of the shaft pilin LrpA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	0.1 M sodium acetate pH 4.6, 15% PEG 3000, 5% polyvinylpyrrolidone K15

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.391	α = 90
b = 47.391	β = 90
c = 227.411	γ = 120

Symmetry
Space Group	P 31

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		2017-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97895	ESRF	ID29

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	2.268	75.804	98.4	0.036	0.038	0.012	1	27.9	10.3		26024

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	2.268	2.307	99.7		0.819	0.86	0.264	0.888	2.5	10.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.27	75.8	24719	1305	98.34	0.22332	0.22227	0.22	0.24019	0.24	RANDOM	69

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]
1.93	0.97		1.93		-6.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.354
r_long_range_B_refined	9.002
r_long_range_B_other	9.002
r_dihedral_angle_1_deg	7.437
r_scangle_other	7.22
r_mcangle_it	5.895
r_mcangle_other	5.893
r_dihedral_angle_2_deg	5.354
r_scbond_it	4.876
r_scbond_other	4.874
r_mcbond_it	4.425
r_mcbond_other	4.418
r_angle_refined_deg	1.264
r_angle_other_deg	0.427
r_chiral_restr	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3036
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing