1ZW5

X-ray structure of Farnesyl diphosphate synthase protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YV5	pdb entry 1YV5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	14% PEG 6000, 0.7 M LiCl, 70 mM citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.255	α = 90
b = 112.255	β = 90
c = 63.245	γ = 90

Symmetry
Space Group	P 41 21 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	MARRESEARCH		2005-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.984	SLS	X10SA

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	2.3	63	95.6	0.1	0.11	13.9	5.2	18323	17517			38

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	97.9		2.7	5.2

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1YV5	2.3	30	17553	16605	886	94.59	0.17508	0.17508	0.17249	0.22311	RANDOM	46.785

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]
-3.86			-3.86		7.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.947
r_dihedral_angle_4_deg	16.52
r_dihedral_angle_3_deg	15.64
r_scangle_it	7.394
r_scbond_it	5.873
r_dihedral_angle_1_deg	5.53
r_mcangle_it	3.529
r_mcbond_it	2.427
r_angle_refined_deg	1.504
r_angle_other_deg	0.84
r_mcbond_other	0.648
r_symmetry_vdw_other	0.239
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.203
r_nbtor_refined	0.185
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.139
r_symmetry_vdw_refined	0.13
r_nbtor_other	0.087
r_chiral_restr	0.079
r_metal_ion_refined	0.047
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2697
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling