3EOE | pdb_00003eoe

Crystal Structure of Pyruvate Kinase from toxoplasma gondii, 55.m00007

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.039	α = 90
b = 130.684	β = 117.4
c = 113.848	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2007-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

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	2.31	50	93.2	0.069	0.053		3.6	110952	103408			49.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.31	2.4	53.8		0.588	0.484	1.2	2.3	5921

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.31	42.68	100883	5074	90.94	0.208	0.206	0.2011	0.253	0.2459	RANDOM	36.264

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]
1.16		-0.47	0.72		-2.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.766
r_dihedral_angle_3_deg	16.361
r_dihedral_angle_4_deg	16.33
r_dihedral_angle_1_deg	5.059
r_scangle_it	1.49
r_angle_refined_deg	1.118
r_scbond_it	0.91
r_mcangle_it	0.497
r_nbtor_refined	0.292
r_mcbond_it	0.289
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.165
r_symmetry_hbond_refined	0.14
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13350
Nucleic Acid Atoms
Solvent Atoms	639
Heterogen Atoms	18

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction