3K4Y

Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IPP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	crystals were grown in 1.6M ammonium sulfate and then transferred to a solution containing 1.6M ammonium sulfate, 10mM IPP, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.09	α = 90
b = 99.23	β = 90
c = 87.41	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	100	CCD	ADSC QUANTUM 315		2008-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.54	50	98.6	0.077	16.32	5.87	22954	22723		-3	47.429

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.54	2.64	89.8		0.489	3.5	5.66	3643

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	CNS rigid body	THROUGHOUT	2.54	43.71	22723	1145	98.99	0.227	0.224	0.287	RANDOM	42.056

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]
0.55			1.44		-1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.697
r_dihedral_angle_3_deg	13.728
r_dihedral_angle_4_deg	12.749
r_dihedral_angle_1_deg	4.631
r_scangle_it	1.333
r_mcangle_it	0.828
r_angle_refined_deg	0.784
r_scbond_it	0.771
r_mcbond_it	0.448
r_chiral_restr	0.054
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4074
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	48

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
XDS	data reduction
CNS	phasing