5JUZ | pdb_00005juz

Crystal structure of human FPPS in complex with an allosteric inhibitor CL-06-057

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.6 M sodium phosphate, 0.6 M potassium phosphate, 25% glycerol, 0.075 M HEPES, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.9	α = 90
b = 110.9	β = 90
c = 77	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	RAYONIX MX-300		2016-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

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	2.4	78.42	99.8	0.098	14.1	9.3		19304			46.933

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	2.4	2.46	99.4		0.931	2.3	9.4

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	FOURIER SYNTHESIS	THROUGHOUT	4QXS	2.4	78.42	18322	951	99.75	0.18285	0.1805	0.19	0.22718	0.23	RANDOM	64.524

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]
-2.84			-2.84		5.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.485
r_dihedral_angle_4_deg	22.427
r_dihedral_angle_3_deg	15.556
r_long_range_B_refined	6.675
r_long_range_B_other	6.674
r_dihedral_angle_1_deg	6.472
r_scangle_other	3.923
r_mcangle_it	2.986
r_mcangle_other	2.985
r_scbond_it	2.515
r_scbond_other	2.515
r_angle_refined_deg	2.135
r_mcbond_it	1.875
r_mcbond_other	1.87
r_angle_other_deg	1.168
r_chiral_restr	0.113
r_bond_refined_d	0.023
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2610
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing