9RU4 | pdb_00009ru4

Crystal structure of a sialic acid binding protein, Q216A mutant, 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	5.4	293	0.1M NaCit, 3.6M ammonium sulfate, pH 5.4

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.831	α = 90
b = 61.493	β = 106.23
c = 89.394	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		2024-11-22	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)	Rrim I (All)	Rpim I (All)	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	1.6	66.78	97.7	0.107	0.04	12.9	7.1		106140			10.64

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	93.7		0.509	0.188	2.2	7.1

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	1.6	66.778	106085	1989	97.671	0.181	0.1803	0.1902	0.2308	0.2413	12.969

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]
2.542		0.396	-0.719		-1.756

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.904
r_dihedral_angle_3_deg	12.89
r_lrange_it	10.913
r_lrange_other	9.585
r_dihedral_angle_2_deg	9.021
r_dihedral_angle_1_deg	5.812
r_scangle_it	5.651
r_scangle_other	5.614
r_mcangle_other	4.03
r_mcangle_it	4.029
r_scbond_it	3.799
r_scbond_other	3.767
r_rigid_bond_restr	2.969
r_mcbond_it	2.736
r_mcbond_other	2.728
r_angle_refined_deg	1.538
r_angle_other_deg	0.573
r_symmetry_nbd_refined	0.245
r_nbd_other	0.226
r_nbd_refined	0.224
r_symmetry_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.185
r_xyhbond_nbd_other	0.168
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_other	0.058
r_ncsr_local_group_1	0.058
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	6229
Nucleic Acid Atoms
Solvent Atoms	1130
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data scaling
REFMAC	phasing