5IN9 | pdb_00005in9

Crystal structure of Grp94 bound to methyl 3-chloro-2-(2-(1-((5-chlorofuran-2-yl)methyl)-1H-imidazol-2-yl)ethyl)-4,6-dihydroxybenzoate, an inhibitor based on the BnIm and Radamide scaffolds.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GFD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	Crystals were grown in 35% PEG 400, 100 mM Tris pH 7.5, 120 mM magnesium chloride. Crystals were harvested and soaked in mother liquor containing 10 mM inhibitor. Glycerol was added and crystals were subsequently cryo-cooled with liquid nitrogen

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.02	α = 90
b = 65.65	β = 92.91
c = 95.86	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	80	IMAGE PLATE	MAR scanner 300 mm plate		2014-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1	APS	22-BM

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	2.6	47.9	100	22.93	7.6		16605

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2GFD	2.6	47.868	1.35	32229	3210	99.92	0.1827	0.1755	0.18	0.2477	0.25

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	17.65
f_angle_d	1.295
f_chiral_restr	0.046
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3467
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	142

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	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.