4JZX

Crystal Structure of Leshmaniasis major Farnesyl diphosphate synthase in complex with 3-BUTYL-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM, IPP and Ca2+

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	6.5	291	PEG 3350, pH 6.5, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.428	α = 90
b = 85.805	β = 90
c = 106.867	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS		2009-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.54178

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	1.8	50	99.8	0.07	10.6	6.8		68699

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)
1	1.8	1.86	99.9		0.545		5.4	6788

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	1.8	25.94	68610	3477	99.78	0.1807	0.1782	0.2272	RANDOM	28.0746

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]
0.9			-0.56		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.669
r_dihedral_angle_3_deg	12.363
r_dihedral_angle_4_deg	10.421
r_dihedral_angle_1_deg	4.286
r_scangle_it	2.317
r_scbond_it	1.472
r_angle_refined_deg	1.108
r_mcangle_it	0.858
r_mcbond_it	0.556
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.669
r_dihedral_angle_3_deg	12.363
r_dihedral_angle_4_deg	10.421
r_dihedral_angle_1_deg	4.286
r_scangle_it	2.317
r_scbond_it	1.472
r_angle_refined_deg	1.108
r_mcangle_it	0.858
r_mcbond_it	0.556
r_nbtor_refined	0.3
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.134
r_symmetry_hbond_refined	0.133
r_metal_ion_refined	0.12
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5752
Nucleic Acid Atoms
Solvent Atoms	776
Heterogen Atoms	74

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection

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.