2G5R | pdb_00002g5r

Crystal structure of Siglec-7 in complex with methyl-9-(aminooxalyl-amino)-9-deoxyNeu5Ac (oxamido-Neu5Ac)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O7S	Siglec-7, APO, 1o7S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	30% PEG 4000, 0.1M sodium acetate, pH 4.6, 0.2M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.928	α = 90
b = 52.928	β = 90
c = 93.236	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2003-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.933	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	25	97.5	0.043	21.5	4.2		17748	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	78.9		0.338	2	2.2

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Siglec-7, APO, 1o7S	1.6	25	17691	893	97.56	0.214	0.214	0.213	0.22	0.228	RANDOM	19.424

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]
0.56			0.56		-1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.027
r_scangle_it	3.311
r_mcangle_it	2.863
r_scbond_it	2.448
r_mcbond_it	1.77
r_angle_refined_deg	1.347
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.149
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.027
r_scangle_it	3.311
r_mcangle_it	2.863
r_scbond_it	2.448
r_mcbond_it	1.77
r_angle_refined_deg	1.347
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.149
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.124
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	904
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.