8WCH | pdb_00008wch

Crystal structure of SAR11_0655 bound to a co-purified ligand, L-pyroglutamate

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, HANGING DROP	3.5	293	1.5 uL 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG 6000 + 1.5 uL 12 mg/mL protein. Cryoprotected in 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG 6000, 30% (v/v) ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.204	α = 90
b = 122.204	β = 90
c = 125.908	γ = 90

Symmetry
Space Group	P 41 21 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 EIGER X 9M		2023-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.000	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.519	43.846	99.9	0.133	0.136	0.999	14.89	20.9		146122

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.52	1.61	99.6		3.18	3.26	0.506	0.95

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	1.519	41.304	146120	7328	99.917	0.152	0.1502	0.16	0.1867	0.2	22.753

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]
-0.04			-0.04		0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.284
r_dihedral_angle_2_deg	14.518
r_dihedral_angle_3_deg	12.877
r_dihedral_angle_1_deg	6.098
r_rigid_bond_restr	3.788
r_lrange_it	3.035
r_lrange_other	2.736
r_scangle_it	2.382
r_scangle_other	2.382
r_mcangle_it	1.96
r_mcangle_other	1.96
r_scbond_it	1.807
r_scbond_other	1.807
r_angle_refined_deg	1.569
r_mcbond_it	1.464
r_mcbond_other	1.464
r_angle_other_deg	0.565
r_symmetry_nbd_refined	0.317
r_symmetry_xyhbond_nbd_refined	0.253
r_nbd_refined	0.226
r_nbd_other	0.207
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.028
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5952
Nucleic Acid Atoms
Solvent Atoms	602
Heterogen Atoms	20

Software

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