8WD5 | pdb_00008wd5

Crystal structure of farnesyl diphosphate synthase FPPS1 from silkworm, Bombyx mori

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UBY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	2% Tacsimate pH 5.0, 0.1 M sodium citrate, pH 5.6, 16% polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.53	α = 90
b = 64.967	β = 92.425
c = 108.378	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS3 6M		2023-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.9792	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.8	45.4	99.6	0.133	0.15	0.069	0.993	9.6	4.8		21918

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	2.8	2.95	100		0.476	0.542	0.253	0.837

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.8	42.365	21898	1026	99.491	0.242	0.2398	0.24	0.2923	0.29	40.376

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]
1.073		-2.425	0.798		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.82
r_dihedral_angle_3_deg	19.445
r_dihedral_angle_4_deg	13.826
r_lrange_it	6.731
r_dihedral_angle_1_deg	6.004
r_scangle_it	4.249
r_mcangle_it	3.352
r_scbond_it	2.594
r_mcbond_it	2.087
r_angle_refined_deg	1.625

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.82
r_dihedral_angle_3_deg	19.445
r_dihedral_angle_4_deg	13.826
r_lrange_it	6.731
r_dihedral_angle_1_deg	6.004
r_scangle_it	4.249
r_mcangle_it	3.352
r_scbond_it	2.594
r_mcbond_it	2.087
r_angle_refined_deg	1.625
r_nbtor_refined	0.293
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.201
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_refined	0.072
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5494
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
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.