Experiment: 4H5E

Crystal structure of human FPPS in ternary complex with YS0470 and isopentenyl pyrophosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DEM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	295	30% PEG 300, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.239	α = 90
b = 111.239	β = 90
c = 65.645	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	IMAGE PLATE	RIGAKU RAXIS IV++		2011-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	2.04	50	100	0.062	47.7	27.3	26486	26486

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	2.04	2.09	100		0.506	6.9	26.2	1289

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	4DEM	2.04	50	24849	24849	1316	98.2	0.18805	0.18805	0.18573	0.1866	0.23334	0.2327	RANDOM	44.763

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]
-2.55			-2.55		5.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.682
r_dihedral_angle_4_deg	16.471
r_dihedral_angle_3_deg	15.098
r_dihedral_angle_1_deg	5.489
r_angle_refined_deg	1.991
r_chiral_restr	0.204
r_bond_refined_d	0.02
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2716
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	43

Software

Software
Software Name	Purpose
StructureStudio	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing