3K56

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	1.6M ammonium sulfate, 5mM ATP gamma-S, 1mM IP, 2mM magnesium chloride., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.68	α = 90
b = 100.24	β = 90
c = 87.79	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	2.34	50	99	0.07	14.65	7.01	29535	29290		-3	57.911

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)
	2.34	2.44	91.7		0.583	3	6.76	4681

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB Entry 3K4O	2.34	42.11	29289	1468	99.45	0.222	0.22	0.259	RANDOM	51.764

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]
0.78			1.59		-2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.819
r_dihedral_angle_3_deg	18.499
r_dihedral_angle_4_deg	16.276
r_dihedral_angle_1_deg	6.817
r_scangle_it	4.63
r_scbond_it	2.896
r_mcangle_it	2.108
r_angle_refined_deg	1.985
r_mcbond_it	1.16
r_chiral_restr	0.118

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.819
r_dihedral_angle_3_deg	18.499
r_dihedral_angle_4_deg	16.276
r_dihedral_angle_1_deg	6.817
r_scangle_it	4.63
r_scbond_it	2.896
r_mcangle_it	2.108
r_angle_refined_deg	1.985
r_mcbond_it	1.16
r_chiral_restr	0.118
r_bond_refined_d	0.02
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4075
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	48

Software

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

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.