8KD0 | pdb_00008kd0

Crystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to a co-purified ligand, beta-galactopyranose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8HQQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	20% (v/v) 2-propanol, 0.1 M MES pH 6.5, 23% (w/v) PEG 1500. 1.2 uL protein + 1.2 uL precipitant.

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.879	α = 90
b = 43.879	β = 90
c = 328.555	γ = 120

Symmetry
Space Group	P 32 2 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 9M		2023-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.0	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	1.67	46.936	99.6	0.135	0.141	0.997	11.08	12.2		43960

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	1.67	1.78	97.3		1.608	1.683	0.864	1.05	11.37

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	8HQQ	1.675	38.029	43950	2217	99.547	0.195	0.1937	0.2	0.2288	0.24	40.44

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]
1.066	0.533		1.066		-3.457

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.733
r_dihedral_angle_3_deg	15.653
r_dihedral_angle_2_deg	15.328
r_dihedral_angle_1_deg	6.252
r_lrange_it	4.404
r_lrange_other	4.401
r_scangle_it	3.909
r_scangle_other	3.908
r_scbond_it	2.664
r_scbond_other	2.663
r_mcangle_it	2.368
r_mcangle_other	2.368
r_mcbond_it	1.864
r_mcbond_other	1.857
r_angle_refined_deg	1.368
r_angle_other_deg	0.484
r_nbd_refined	0.215
r_symmetry_nbd_refined	0.208
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.159
r_nbd_other	0.139
r_xyhbond_nbd_refined	0.118
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.067
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2933
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	12

Software

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