2ZE6

Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with substrate analog, DMASPP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	277	1.4-2.0M sodium formate, 5mM magnesium chloride, 0.1M sodium acetate buffer, 20mM dimethylallyl S-thiolodiphosphate, pH 4.8-5.4., VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.417	α = 90
b = 96.417	β = 90
c = 65.068	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	RIGAKU JUPITER 210		2004-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45PX	1.0000	SPring-8	BL45PX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	68.2	98.29				17222			24.01

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	FOURIER SYNTHESIS	THROUGHOUT	2.1	68.2	17222	934	98.29	0.19957	0.19633	0.26424	RANDOM	52.277

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]
3.08			3.08		-6.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.323
r_dihedral_angle_4_deg	21.642
r_dihedral_angle_3_deg	19.523
r_dihedral_angle_1_deg	7.028
r_scangle_it	5.124
r_scbond_it	3.615
r_angle_refined_deg	2.605
r_mcangle_it	2.112
r_mcbond_it	1.373
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.323
r_dihedral_angle_4_deg	21.642
r_dihedral_angle_3_deg	19.523
r_dihedral_angle_1_deg	7.028
r_scangle_it	5.124
r_scbond_it	3.615
r_angle_refined_deg	2.605
r_mcangle_it	2.112
r_mcbond_it	1.373
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.274
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.159
r_symmetry_vdw_refined	0.155
r_chiral_restr	0.153
r_bond_refined_d	0.026
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1824
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.