2ZE5 | pdb_00002ze5

Crystal Structure of adenosine phosphate-isopentenyltransferase

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

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.392	α = 90
b = 96.392	β = 90
c = 65.197	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		2004-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45PX	0.9792	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	2.31	68.2	97.9				13741			42.545

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	68.2	13059	682	97.87	0.2035	0.20098	0.1984	0.25433	0.2505	RANDOM	44.708

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]
2.08			2.08		-4.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.404
r_dihedral_angle_4_deg	19.064
r_dihedral_angle_3_deg	17.252
r_dihedral_angle_1_deg	6.638
r_scangle_it	4.753
r_scbond_it	3.243
r_angle_refined_deg	2.258
r_mcangle_it	1.855
r_mcbond_it	1.19
r_nbtor_refined	0.312
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.168
r_symmetry_vdw_refined	0.141
r_chiral_restr	0.137
r_bond_refined_d	0.027
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1824
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	24

Software

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