6B07 | pdb_00006b07

Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl diphosphate synthase, complexed with [1-phosphono-2-(1-propylpyridin-2-yl)ethyl]phosphonic acid (inhibitor 1d)

X-RAY DIFFRACTION

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	MICROBATCH		295	20% PEG3350, 0.2 M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.913	α = 90
b = 122.579	β = 106.51
c = 69.064	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	100	CCD	RIGAKU SATURN 944		2015-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.98	101.18	96	0.069	0.08	0.041	9.3	3.7		99585

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.05	82		0.536	0.643	0.351	0.735		3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 1YV5	1.98	101.18	94476	4966	95.86	0.1728	0.1709	0.18	0.2089	0.22	RANDOM	32.884

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]
0.33		-0.13	-0.42		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.434
r_dihedral_angle_4_deg	19.77
r_dihedral_angle_3_deg	15.129
r_dihedral_angle_1_deg	5.562
r_angle_refined_deg	1.915
r_angle_other_deg	1.15
r_chiral_restr	0.134
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.434
r_dihedral_angle_4_deg	19.77
r_dihedral_angle_3_deg	15.129
r_dihedral_angle_1_deg	5.562
r_angle_refined_deg	1.915
r_angle_other_deg	1.15
r_chiral_restr	0.134
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8148
Nucleic Acid Atoms
Solvent Atoms	911
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	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.