5UMC | pdb_00005umc

Synthesis of novel seleno ureido containing compounds as SLC-0111 analogs. Investigations on carbonic anhydrases activity, glutathione peroxidase and X-ray crystallography

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		281	concentrated CA II at ~10 mg/mL was set up in SD-2 plates (Molecular Dimensions) with the following ratio of protein plus reservoir plus seeds: 250 nL + 225 nL + 25 nL. The plate was incubated at 8 C and the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3. Dry compound was added to the crystallization drop after crystals had formed and several days before data were collected.

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.485	α = 90
b = 41.498	β = 104.42
c = 72.28	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 210		2016-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	1.00800	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.15	41.5	99.3	0.225	0.112	0.978	5.7	5		13493

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21	92.4		0.793	0.396	0.755	2	4.8

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	4cq0	2.15	41.5	12801	680	99.29	0.19944	0.19628	0.2	0.26112	0.26	RANDOM	20.219

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]
-1.04		0.42	-2.36		2.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.798
r_dihedral_angle_4_deg	20.734
r_dihedral_angle_3_deg	16.081
r_dihedral_angle_1_deg	6.949
r_long_range_B_refined	4.269
r_long_range_B_other	4.269
r_scangle_other	2.564
r_mcangle_other	2.155
r_mcangle_it	2.154
r_angle_refined_deg	1.658
r_scbond_other	1.575
r_scbond_it	1.573
r_mcbond_it	1.331
r_mcbond_other	1.328
r_angle_other_deg	1
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2059
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	35

Software

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