9RSL | pdb_00009rsl

Crystal structure of a sialic acid binding protein, R113A 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
2.15	42.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.347	α = 90
b = 89.404	β = 90
c = 151.269	γ = 90

Symmetry
Space Group	P 21 21 21

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	1.7	57.74	100	0.184	0.049	8.5	13.6		92279			11.65

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	1.7	1.73	98.3		1.018	0.273	1.4	13.7

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	1.7	57.74	92170	2016	99.935	0.172	0.1715	0.1762	0.1982	0.2025	15.332

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]
-1.349			-0.931		2.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.481
r_dihedral_angle_3_deg	11.968
r_dihedral_angle_2_deg	8.176
r_lrange_it	5.983
r_dihedral_angle_1_deg	5.794
r_lrange_other	5.571
r_scangle_it	4.097
r_scangle_other	4.014
r_scbond_it	2.598
r_scbond_other	2.502
r_mcangle_other	1.806
r_mcangle_it	1.805
r_angle_refined_deg	1.511
r_mcbond_it	1.208
r_mcbond_other	1.206
r_angle_other_deg	0.554
r_nbd_refined	0.24
r_nbd_other	0.231
r_symmetry_nbd_refined	0.228
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.176
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_other	0.06
r_ncsr_local_group_1	0.047
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	6253
Nucleic Acid Atoms
Solvent Atoms	1322
Heterogen Atoms	69

Software

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