4K10 | pdb_00004k10

Crystal Structure of Leshmaniasis major Farnesyl diphosphate synthase in complex with 3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM and Mg2+

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG 3350 15-25%, 100 mM MES pH 6.5, 100-200 mM CaAcetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.168	α = 90
b = 143.743	β = 90
c = 194.333	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	CCD	RAYONIX MX-225	KB Rh, Pt, ULE	2009-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97929	APS	31-ID

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	2.3	115.47	91.2	0.106	14.1	5.6		69237

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	2.3	2.38	96.5		0.675		4.9

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		THROUGHOUT	2.3	115.47	67927	3410	89.63	0.2352	0.2331	0.23	0.276	0.27	RANDOM	48.821

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]
-2.35			5.06		-2.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.352
r_dihedral_angle_3_deg	16.815
r_dihedral_angle_4_deg	14.609
r_dihedral_angle_1_deg	5.084
r_scangle_it	2.074
r_scbond_it	1.324
r_angle_refined_deg	1.258
r_mcangle_it	0.957
r_mcbond_it	0.515
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.352
r_dihedral_angle_3_deg	16.815
r_dihedral_angle_4_deg	14.609
r_dihedral_angle_1_deg	5.084
r_scangle_it	2.074
r_scbond_it	1.324
r_angle_refined_deg	1.258
r_mcangle_it	0.957
r_mcbond_it	0.515
r_nbtor_refined	0.298
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.204
r_metal_ion_refined	0.189
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.098
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11389
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	113

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
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.