4RXA

Crystal structure of human farnesyl diphosphate synthase in complex with BPH-1358

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	1.2M NA/K phosphate, 25% glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.757	α = 90
b = 110.757	β = 90
c = 77.96	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	298	CCD	MARMOSAIC 300 mm CCD		2014-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

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	2.2	55.41	100				20748	1	1

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)
1	2.2	2.4	100		0.472

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.2	78.32	1152	94.32	0.2234	0.2213	0.2629	RANDOM	27.135

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]
0.85			0.85		-1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.977
r_dihedral_angle_4_deg	20.212
r_dihedral_angle_3_deg	17.821
r_dihedral_angle_1_deg	6.76
r_mcangle_it	2.507
r_mcbond_it	1.696
r_mcbond_other	1.69
r_angle_refined_deg	0.896
r_angle_other_deg	0.573
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.977
r_dihedral_angle_4_deg	20.212
r_dihedral_angle_3_deg	17.821
r_dihedral_angle_1_deg	6.76
r_mcangle_it	2.507
r_mcbond_it	1.696
r_mcbond_other	1.69
r_angle_refined_deg	0.896
r_angle_other_deg	0.573
r_chiral_restr	0.069
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2659
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASES	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.