2ZE8

Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate

X-RAY DIFFRACTION

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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 diphosphate, pH 4.8-5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.51	α = 90
b = 97.568	β = 90
c = 131.108	γ = 90

Symmetry
Space Group	P 21 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		2004-01-01	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	2.8	131.31	97.83				29244			39.384

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	2.8	131.31	29244	1566	97.83	0.23385	0.2303	0.30218	RANDOM	85.639

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]
3.88			4.1		-7.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.186
r_dihedral_angle_4_deg	24.805
r_dihedral_angle_3_deg	24.088
r_dihedral_angle_1_deg	8.853
r_angle_refined_deg	2.975
r_mcangle_it	1.884
r_scangle_it	1.818
r_scbond_it	1.15
r_mcbond_it	1.148
r_nbtor_refined	0.377
r_symmetry_vdw_refined	0.375
r_symmetry_hbond_refined	0.368
r_nbd_refined	0.337
r_xyhbond_nbd_refined	0.272
r_chiral_restr	0.169
r_bond_refined_d	0.032
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7260
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	36

Software

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