3MNR | pdb_00003mnr

Crystal Structure of Benzamide SNX-1321 bound to Hsp90

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D0B	PDB ENTRY 3D0B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	6.5	277	Crystallized in 0.2M MgCl2, 0.1M Bis-Tris pH 6.5, and 20% PEG 3350 and were cryo-protected by adding 25% Ethylene Glycol to the mother liquor and passing the crystal through the solution immediately before flash freezing it in liquid nitrogen. The drops were setup by hand, adding 0.5ul protein to 0.5ul of reservoir in a sitting drop 192-well corning crystallization plate and incubated at 277K. , LIQUID DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.773	α = 90
b = 90.753	β = 90
c = 99.116	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113.5	CCD	RIGAKU SATURN 92		2004-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.9	36.45	95	0.084	10.8	2.74	23062	21887	3	10.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.97	95		0.13	1.8	1.8

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3D0B	1.9	36.45	23062	21887	1175	95.56	0.19021	0.18784	0.192	0.23458	RANDOM	20.528

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]
-0.24			0.7		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.964
r_dihedral_angle_4_deg	20.326
r_dihedral_angle_3_deg	12.74
r_dihedral_angle_1_deg	5.831
r_scangle_it	2.59
r_scbond_it	1.589
r_angle_refined_deg	1.302
r_mcangle_it	1.111
r_mcbond_it	0.671
r_nbtor_refined	0.301
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.171
r_symmetry_hbond_refined	0.125
r_xyhbond_nbd_refined	0.103
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1644
Nucleic Acid Atoms
Solvent Atoms	345
Heterogen Atoms	35

Software

Software
Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling