7UI8 | pdb_00007ui8

Intramolecular ester bond-containing repeat domain from E. columbae adhesin (split and religated)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NI6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	3.2 M ammonium sulfate, 0.1 M sodium citrate, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.775	α = 90
b = 120.775	β = 90
c = 45.444	γ = 120

Symmetry
Space Group	P 6 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 EIGER2 S 16M		2022-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95366	Australian Synchrotron	MX2

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	2.37	45.44	99.4	0.187	0.193	0.045	0.998	12	18.6		8323			53.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.37	2.46	94.5		0.593	0.806	0.9	17.6

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	4NI6	2.373	40.003	8247	401	98.956	0.228	0.226	0.23	0.2614	0.27	59.756

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]
0.035	0.017		0.035		-0.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.379
r_dihedral_angle_4_deg	23.493
r_dihedral_angle_3_deg	15.439
r_dihedral_angle_1_deg	7.257
r_lrange_it	6.61
r_lrange_other	6.605
r_scangle_it	5.197
r_scangle_other	5.194
r_mcangle_it	3.631
r_mcangle_other	3.63
r_scbond_it	3.296
r_scbond_other	3.293
r_mcbond_it	2.321
r_mcbond_other	2.317
r_angle_refined_deg	1.299
r_angle_other_deg	1.13
r_nbd_other	0.188
r_nbd_refined	0.182
r_symmetry_nbd_other	0.167
r_symmetry_nbd_refined	0.163
r_nbtor_refined	0.139
r_symmetry_xyhbond_nbd_refined	0.131
r_xyhbond_nbd_refined	0.12
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.037
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1016
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms

Software

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