4MAG

Crystal structure of the Periplasmic Sialic Acid Binding Protein from Vibrio Cholerea

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B50	PDB ENTRY 3B50

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	36 mg/ml SiaP in 20 mM HEPES, 10 mM sodium chloride, pH 8.0 and reservoir solution (0.1 M MES, 20% w/v PEG-6000 at pH 6.0). , VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.977	α = 90
b = 82.315	β = 90
c = 119.354	γ = 90

Symmetry
Space Group	I 2 2 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	MAR CCD 165 mm		2006-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.9793	APS	23-ID-B

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	1.45	19.91	99.8	0.073	7.9	6.04	65540	65409			24.6

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	1.45	1.5	100		0.655	1.8	5.97	6477

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3B50	1.45	11.73	65331	3314	99.82	0.184	0.184	0.1822	0.2194	RANDOM	29.4153

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]
-0.34			-0.45		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.568
r_dihedral_angle_4_deg	14.508
r_dihedral_angle_3_deg	11.603
r_dihedral_angle_1_deg	4.906
r_scangle_it	3.595
r_scbond_it	2.484
r_mcangle_it	1.49
r_mcbond_it	1.267
r_angle_refined_deg	1.233
r_angle_other_deg	0.896
r_mcbond_other	0.373
r_symmetry_vdw_refined	0.234
r_symmetry_vdw_other	0.222
r_nbd_refined	0.21
r_nbd_other	0.185
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.151
r_nbtor_other	0.086
r_chiral_restr	0.076
r_xyhbond_nbd_other	0.025
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2445
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	6

Software

Software
Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
AMoRE	phasing