2JHD

Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 3'-sialyl-N-acetyllactosamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JH1	PDB ENTRY 2JH1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7		VAPOUR DIFFUSION IN HANGING DROP 3.4 M AMMONIUM ACETATE 100 MM BIS-TRIS-PROPANE PH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.48	64.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.132	α = 90
b = 66.132	β = 90
c = 172.681	γ = 90

Symmetry
Space Group	P 43 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 CCD	COLLIMATOR, MONOCHROMATOR, MIRROR	2006-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1		SRS	PX14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.3	18	100	0.09	38	7.6		17796		-3.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	99.9		0.41	6.7	7.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2JH1	2.3	17.5	16806	915	100	0.175	0.173	0.213	RANDOM	35.84

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]
-0.01			-0.01		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.783
r_dihedral_angle_3_deg	15.771
r_dihedral_angle_4_deg	10.247
r_dihedral_angle_1_deg	6.929
r_scangle_it	4.787
r_scbond_it	3.184
r_mcangle_it	2.143
r_angle_refined_deg	1.885
r_mcbond_it	1.373
r_nbtor_refined	0.301
r_nbd_refined	0.219
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.188
r_symmetry_vdw_refined	0.183
r_chiral_restr	0.132
r_bond_refined_d	0.023
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1719
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing