9RSI | pdb_00009rsi

Crystal structure of a sialic acid binding protein from Streptococcus pneumoniae bound to Neu5Ac

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, SITTING DROP	5	293	0.1 M Sodium citrate, pH 5, 3.2 M Ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.742	α = 90
b = 61.782	β = 106.39
c = 89.603	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 EIGER2 XE 16M		2023-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

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	1.8	67.453	100	0.2	0.217	0.082	0.992	6.4	7		77720

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	1.8	1.84	100		1.281	1.384	0.52	0.717		6.9

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	67.453	77657	3810	99.937	0.165	0.1627	0.1771	0.2049	0.2152	16.772

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]
2.404		0.215	-0.455		-1.769

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.513
r_dihedral_angle_3_deg	11.906
r_dihedral_angle_2_deg	7.175
r_dihedral_angle_1_deg	6.152
r_lrange_it	5.216
r_lrange_other	5.074
r_scangle_it	4.158
r_scangle_other	4.154
r_scbond_it	2.604
r_scbond_other	2.59
r_mcangle_it	1.929
r_mcangle_other	1.928
r_angle_refined_deg	1.6
r_mcbond_it	1.315
r_mcbond_other	1.312
r_angle_other_deg	0.578
r_nbd_other	0.221
r_nbd_refined	0.22
r_nbtor_refined	0.183
r_symmetry_nbd_refined	0.182
r_symmetry_nbd_other	0.181
r_symmetry_xyhbond_nbd_refined	0.174
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.074
r_xyhbond_nbd_other	0.032
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6273
Nucleic Acid Atoms
Solvent Atoms	956
Heterogen Atoms	52

Software

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