4JZB

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.361	α = 90
b = 85.967	β = 90
c = 107.074	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		2009-07-22	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	1.9	66.96	99.4	0.072	11.5	6.8		58810

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	1.9	1.97	95.3		0.473		4.1	5551

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	66.96	58732	2971	99.35	0.1746	0.1727	0.2097	RANDOM	23.043

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]
0.72			-0.67		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.973
r_dihedral_angle_3_deg	12.503
r_dihedral_angle_4_deg	9.251
r_dihedral_angle_1_deg	4.298
r_scangle_it	2.667
r_scbond_it	1.71
r_mcangle_it	1.181
r_angle_refined_deg	1.076
r_mcbond_it	0.6
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.973
r_dihedral_angle_3_deg	12.503
r_dihedral_angle_4_deg	9.251
r_dihedral_angle_1_deg	4.298
r_scangle_it	2.667
r_scbond_it	1.71
r_mcangle_it	1.181
r_angle_refined_deg	1.076
r_mcbond_it	0.6
r_nbtor_refined	0.298
r_nbd_refined	0.192
r_symmetry_vdw_refined	0.165
r_metal_ion_refined	0.162
r_xyhbond_nbd_refined	0.116
r_symmetry_hbond_refined	0.115
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5752
Nucleic Acid Atoms
Solvent Atoms	696
Heterogen Atoms	82

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
AMoRE	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 R01GM157729.