8F9L

Intramolecular ester bond-containing repeat domain from Gemella massiliensis adhesin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.2 M NaCl, 0.1 M Tris.HCl pH 8.0, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.164	α = 90
b = 63.037	β = 90
c = 96.488	γ = 90

Symmetry
Space Group	P 21 21 21

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		2022-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95374	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.78	48.24	99.5	0.999	9.7	13.2		27465

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.82	91.2		0.449	0.6	11.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.788	41.643	27103	1307	99.097	0.233	0.2313	0.265	random selection	34.288

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]
-0.922			0.469		0.453

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.781
r_dihedral_angle_3_deg	11.789
r_dihedral_angle_1_deg	6.936
r_lrange_it	3.24
r_lrange_other	3.234
r_scangle_other	2.245
r_scangle_it	2.238
r_mcangle_it	1.585
r_mcangle_other	1.584
r_scbond_other	1.366
r_scbond_it	1.363
r_mcbond_it	1.005
r_mcbond_other	1.004
r_angle_refined_deg	0.956
r_angle_other_deg	0.326
r_symmetry_nbd_refined	0.273
r_symmetry_xyhbond_nbd_refined	0.234
r_nbd_refined	0.204
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.162
r_nbd_other	0.16
r_xyhbond_nbd_refined	0.122
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.041
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2116
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	10

Software

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