1YHK | pdb_00001yhk

Trypanosoma cruzi farnesyl diphosphate synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Selenomethionine replaced protein model (MAD)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	4.6	293	pH 4.6, LIQUID DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	47.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.925	α = 90
b = 57.925	β = 90
c = 397.697	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				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97929	NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	65.94					21828

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Selenomethionine replaced protein model (MAD)	2.1	65.94	21828	21828	1172	93.95	0.17581	0.17308	0.22686	RANDOM	27.413

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]
0.56	0.28		0.56		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.954
r_dihedral_angle_1_deg	5.644
r_scbond_it	3.811
r_mcangle_it	2.385
r_angle_refined_deg	2.088
r_mcbond_it	1.361
r_angle_other_deg	1.056
r_symmetry_vdw_other	0.327
r_nbd_other	0.251
r_symmetry_vdw_refined	0.234
r_nbd_refined	0.231
r_symmetry_hbond_refined	0.225
r_xyhbond_nbd_refined	0.193
r_chiral_restr	0.144
r_nbtor_other	0.093
r_bond_refined_d	0.031
r_gen_planes_refined	0.012
r_gen_planes_other	0.007
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2873
Nucleic Acid Atoms
Solvent Atoms	280
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing