1QK5 | pdb_00001qk5

TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH XMP, PYROPHOSPHATE AND TWO MG2+ IONS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QK3	PDB ENTRY 1QK3, SUBUNIT A, WITHOUT LOOPS, WATERS, OR GMP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	277	30% PEG 4000, 100 MM TRIS.CL (PH 8.5), 200 MM LI2SO4, 0.25 % BETA-OCTYLGLUCOPYRANOSIDE. THE CRYSTAL WAS GROWN IN THE PRESENCE OF 1 MM XANTHINE, 1 MM PRPP AND 10 MM MGCL2 AT 277 K.

Crystal Properties
Matthews coefficient	Solvent content
2.09	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.208	α = 90
b = 112.255	β = 90
c = 144.28	γ = 90

Symmetry
Space Group	C 2 2 21

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	PRINCETON SCIENTIFIC INSTRUMENTS 2K CCD	PT-COATED MIRROR	1998-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25

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	1.6	13	98	0.076	10.3	4.2		58200			24.14

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	1.6	1.66	93.9		0.373	2.4	3.7

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-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QK3, SUBUNIT A, WITHOUT LOOPS, WATERS, OR GMP	1.6	13	55139	2953	98	0.23351	0.26099	RANDOM	25.06

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_scangle_it	3.53
p_mcangle_it	2.466
p_scbond_it	2.282
p_mcbond_it	1.709
p_chiral_restr	0.147
p_angle_d	0.04
p_planar_d	0.038
p_bond_d	0.015
p_plane_restr	0.012
p_angle_deg
p_hb_or_metal_coord
p_singtor_nbd
p_multtor_nbd
p_xhyhbond_nbd
p_xyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3472
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing