7X6F | pdb_00007x6f

Outer membrane lipoprotein QseG of Escherichia coli O157:H7

X-RAY DIFFRACTION

---

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		293	0.08 M magnesium acetate tetrahydrate, 0.1 M sodium citrate pH 6.0, 14% (w/v) polyethylene glycol monomethyl ether 5000

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.963	α = 90
b = 149.785	β = 94.649
c = 88.302	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 EIGER X 16M		2021-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9000	SPring-8	BL44XU

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	2.3	43.43	98.9	0.091	0.108	0.058	0.996	8.5	3.4		48807

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	2.3	2.38	99.7		0.834	0.983	0.516	0.65	1.6	3.6

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	AlphaFold structure	2.3	39.803	48774	2466	98.839	0.223	0.2206	0.22	0.2735	0.27	52.887

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]
-0.095		-0.031	-0.006		0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.122
r_dihedral_angle_3_deg	21.163
r_dihedral_angle_4_deg	20.35
r_lrange_it	9.305
r_scangle_it	9.106
r_scbond_it	7.534
r_mcangle_it	6.625
r_mcbond_it	5.606
r_dihedral_angle_1_deg	5.332
r_angle_refined_deg	1.513
r_nbtor_refined	0.315
r_xyhbond_nbd_refined	0.245
r_symmetry_xyhbond_nbd_refined	0.231
r_nbd_refined	0.23
r_symmetry_nbd_refined	0.206
r_chiral_restr	0.065
r_metal_ion_refined	0.019
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7281
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing