3T07

Crystal structure of S. aureus Pyruvate Kinase in complex with a naturally occurring bis-indole alkaloid

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SITTING DROP	8.5	293	15-20% PEG3350, 0.4 M sodium malonate, 0.1 M bicine, pH 8.5, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.96	α = 86.05
b = 111.91	β = 72.14
c = 112.03	γ = 80.88

Symmetry
Space Group	P 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 225 mm CCD	mirrors	2009-08-14		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-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	3.3	110.47	93.4	0.059	10.2	3.1	53839	53839

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	3.3	3.48	90.1		0.689	0.689	1.1	2.9	7594

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.3	60	53838	2729	93.43	0.1998	0.1983	0.2259	RANDOM	146.8076

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]
2.38	-1.28	-1.19	0.83	-3.16	-1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.054
r_dihedral_angle_3_deg	15.504
r_dihedral_angle_4_deg	14.229
r_dihedral_angle_1_deg	6.29
r_angle_refined_deg	1.413
r_angle_other_deg	0.925
r_chiral_restr	0.067
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.054
r_dihedral_angle_3_deg	15.504
r_dihedral_angle_4_deg	14.229
r_dihedral_angle_1_deg	6.29
r_angle_refined_deg	1.413
r_angle_other_deg	0.925
r_chiral_restr	0.067
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17628
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	74

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxDC	data collection

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 R01GM133198.