9G17 | pdb_00009g17

Structure of PslG with a covalently- bound pentasaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZN2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6	277	20 mM MES pH 6.0, 50 mM sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.692	α = 90
b = 97.692	β = 90
c = 119.775	γ = 120

Symmetry
Space Group	P 65

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 XE 9M		2023-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.95392	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.55	84.604	100	0.155	0.057	0.999	11	16.2		93736

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	1.55	1.58	99.9		0.926	0.663		16.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.55	84.604	93683	4697	99.947	0.143	0.1419	0.1388	0.1739	0.1722	RANDOM	23.288

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]
0.361	0.181		0.361		-1.171

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.429
r_dihedral_angle_6_deg	15.041
r_dihedral_angle_3_deg	11.119
r_scangle_it	9.517
r_dihedral_angle_2_deg	7.766
r_scbond_it	7.084
r_dihedral_angle_1_deg	6.332
r_mcangle_it	6.077
r_rigid_bond_restr	5.225
r_mcbond_it	4.452
r_angle_refined_deg	1.738
r_nbtor_refined	0.319
r_nbd_refined	0.205
r_symmetry_nbd_refined	0.19
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.152
r_chiral_restr	0.126
r_bond_refined_d	0.013
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3309
Nucleic Acid Atoms
Solvent Atoms	632
Heterogen Atoms	95

Software

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