3DYF | pdb_00003dyf

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461 and Isopentyl Diphosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.75	298	10% MPD, 0.1 AMMONIUM ACETATE, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.939	α = 90
b = 117.898	β = 111.27
c = 63.274	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	123.2	CCD	ADSC QUANTUM 4		2006-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C		NSLS	X8C

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	2.65	30	100	0.138	8.4	6.7		26721			37.6

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)
	2.65	2.74	100		0.589		6.5

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.65	29.48	25447	1244	95.5	0.201	0.201	0.2	0.268	0.26	RANDOM	42.1

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]
5.59		6.31	-9.05		3.45

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18
c_scangle_it	8.41
c_scbond_it	6.57
c_mcangle_it	6.33
c_mcbond_it	4.5
c_angle_deg	1.1
c_improper_angle_d	0.74
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5733
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms	78

Software

Software
Software Name	Purpose
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling