5CG6 | pdb_00005cg6

Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate and isopentenyl pyrophosphate

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CG5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.0 M NaCl, 0.08 M sodium acetate, 0.02 M acetic acid

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.627	α = 90
b = 111.627	β = 90
c = 72.553	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	293	CCD	ADSC QUANTUM 210r		2014-06-14	M	SINGLE WAVELENGTH
2	1	neutron	293	IMAGE PLATE	CUSTOM-MADE		2014-03-06	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1	Photon Factory	AR-NW12A
2	NUCLEAR REACTOR		3.2-6.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (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	1.7	44.31	97.7	0.097							8.6		49965
2	2.4	22.16	98.1	0.198							2.8		18171

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.73		0.777							6.4
	2.4	2.49		0.379							2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	MOLECULAR REPLACEMENT	1.7	35.3			49901	49901	2499	96.85		0.1974	0.1966	0.2011	0.2113	0.2101
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.4	22.119			18151	18151	904	98.44		0.2613	0.2599		0.2866

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.852
f_angle_d	1.082
f_chiral_restr	0.183
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2765
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	34

Software

Software
Software Name	Purpose
PHENIX	refinement
STARGazer	data reduction
HKL-2000	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.