3ICM | pdb_00003icm

Trypanosoma cruzi farnesyl diphosphate synthase homodimer in complex with isopentenyl pyrophosphate, Mg2+ and 1-(2-Hydroxy-2,2-bis-phosphono-ethyl)-3-phenyl-pyridinium

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	PEG 4000, 200mM Ammonium Sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.335	α = 90
b = 58.335	β = 90
c = 394.229	γ = 120

Symmetry
Space Group	P 61 2 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		2005-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.1	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	50		0.75	0.75		10.3		27660

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07			0.43	0.43		3.3

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	FOURIER SYNTHESIS	THROUGHOUT	2.2	40.05	21540	1077	99.69	0.19	0.186	0.19	0.254	0.26	RANDOM	33.592

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]
0.18	0.09		0.18		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.679
r_dihedral_angle_4_deg	19.717
r_dihedral_angle_3_deg	16.174
r_dihedral_angle_1_deg	5.644
r_scangle_it	4.282
r_scbond_it	2.872
r_angle_refined_deg	1.814
r_mcangle_it	1.719
r_mcbond_it	1.176
r_symmetry_hbond_refined	0.329

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.679
r_dihedral_angle_4_deg	19.717
r_dihedral_angle_3_deg	16.174
r_dihedral_angle_1_deg	5.644
r_scangle_it	4.282
r_scbond_it	2.872
r_angle_refined_deg	1.814
r_mcangle_it	1.719
r_mcbond_it	1.176
r_symmetry_hbond_refined	0.329
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.242
r_nbd_refined	0.235
r_xyhbond_nbd_refined	0.233
r_chiral_restr	0.132
r_metal_ion_refined	0.092
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2891
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	45

Software

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

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.