6CEH | pdb_00006ceh

Design, Synthesis, X-ray and Biological Activities of Selenides Bearing the Benzenesulfonamide Moiety as New Class of Agents for Prevention of Diabetic Cerebrovascular Pathology

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CQ0	PDB ENTRY 4CQ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		281	200 nL 7 mg/mL protein + 200 nL reservoir solution (2.9 M ammonium sulfate, 100 mM Tris buffer, pH 8.3), equilibriated at 281K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.452	α = 90
b = 41.485	β = 104.49
c = 72.455	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	CCD	ADSC QUANTUM 210r		2017-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.953700	Australian Synchrotron	MX1

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	1.43	41.5	99.3	0.092	17.1	7.1		45001

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	1.43	1.46	95.9		0.59	3.3	6.8

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4CQ0	1.43	41.5	42805	2100	99.1	0.155	0.152	0.15	0.208	0.21	RANDOM	11.03

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]
-0.26		0.11	-0.11		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.613
r_sphericity_free	22.796
r_dihedral_angle_4_deg	21.798
r_dihedral_angle_3_deg	11.285
r_sphericity_bonded	8.268
r_dihedral_angle_1_deg	6.651
r_long_range_B_refined	2.992
r_long_range_B_other	2.992
r_rigid_bond_restr	2.493
r_scangle_other	2.309
r_scbond_it	2.027
r_scbond_other	1.974
r_angle_refined_deg	1.916
r_mcangle_other	1.517
r_mcangle_it	1.505
r_mcbond_it	1.266
r_mcbond_other	1.249
r_angle_other_deg	1.057
r_chiral_restr	0.131
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_bond_other_d	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2064
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing