4IR8

1.85 Angstrom Crystal Structure of Putative Sedoheptulose-1,7 bisphosphatase from Toxoplasma gondii

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	295	Protein: 20.0mG/mL, 0.5M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: PEG's (A2), 0.1M Sodium acetate (pH 4.6), 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.4	α = 90
b = 64.4	β = 90
c = 591.61	γ = 120

Symmetry
Space Group	P 65 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	MARMOSAIC 300 mm CCD	Mirrors	2011-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97903	APS	21-ID-D

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	1.85	30	99.4	0.088	29.6	14.3	64336	64336		-3	23.6

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	1.85	1.88	99.3		0.606	5.3	15	3115

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	3KBZ	1.85	29.52	61040	61040	3242	99.6	0.1558	0.1558	0.15425	0.18465	RANDOM	20.557

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]
0.59	0.29		0.59		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.954
r_dihedral_angle_4_deg	12.809
r_dihedral_angle_3_deg	9.449
r_scangle_it	4.359
r_dihedral_angle_1_deg	3.278
r_scbond_it	2.715
r_mcangle_it	1.676
r_angle_refined_deg	1.323
r_mcbond_it	0.966
r_angle_other_deg	0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.954
r_dihedral_angle_4_deg	12.809
r_dihedral_angle_3_deg	9.449
r_scangle_it	4.359
r_dihedral_angle_1_deg	3.278
r_scbond_it	2.715
r_mcangle_it	1.676
r_angle_refined_deg	1.323
r_mcbond_it	0.966
r_angle_other_deg	0.83
r_mcbond_other	0.304
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4828
Nucleic Acid Atoms
Solvent Atoms	540
Heterogen Atoms	32

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	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.