5BXI | pdb_00005bxi

1.7 Angstrom Resolution Crystal Structure of Putative Nucleoside Diphosphate Kinase from Toxoplasma gondii with Tyrosine of Tag Bound to Active Site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O0N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	Protein:7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: PACT (B10), 0.2 M Magnesium chloride, 0.1 M MES pH 6.0, 20% (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 236.814	α = 90
b = 73.4	β = 116.83
c = 122.671	γ = 90

Symmetry
Space Group	C 1 2 1

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		2015-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97890	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	30	98.5	0.059	0.059	22	4.9	202729	202729		-3	28

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	1.7	1.73	99.9		0.482	3.2	4.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4O0N	1.7	29.98	192440	10203	98.23	0.15551	0.15361	0.16	0.1917	0.2	RANDOM	33.435

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]
-0.66		0.04	1.74		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.188
r_dihedral_angle_4_deg	16.653
r_dihedral_angle_3_deg	10.952
r_long_range_B_refined	6.765
r_long_range_B_other	6.765
r_dihedral_angle_1_deg	3.858
r_scangle_other	3.38
r_scbond_it	2.258
r_scbond_other	2.256
r_mcangle_it	2.218
r_mcangle_other	2.218
r_mcbond_it	1.499
r_mcbond_other	1.499
r_angle_refined_deg	1.398
r_angle_other_deg	0.79
r_chiral_restr	0.092
r_gen_planes_refined	0.022
r_gen_planes_other	0.017
r_bond_refined_d	0.01
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14647
Nucleic Acid Atoms
Solvent Atoms	1854
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BLU-MAX	data collection
PHASER	phasing