5G0C

An unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition and protein x-ray structure of Psammaplin C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A6HPDB ENTRY 5A6H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5SITTING DROP PLATES WITH 200 NL PROTEIN AT 5 MG/ML AND 200 NL RESERVOIR WITH 2.6 TO 2.8 M AMMONIUM SULFATE AND 100 MM TRIS AT PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.0840.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.885α = 90
b = 41.263β = 104.19
c = 71.681γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2015-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX1Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2841.397.40.0715.87.359861
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.281.390.60.692.36.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5A6H1.2869.557012284297.430.131430.129920.1631RANDOM13.377
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]
0.41-0.11-0.27-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.496
r_sphericity_free32.026
r_dihedral_angle_4_deg17.637
r_dihedral_angle_3_deg12.032
r_sphericity_bonded9.16
r_dihedral_angle_1_deg6.943
r_rigid_bond_restr3.985
r_long_range_B_refined3.734
r_long_range_B_other3.733
r_scangle_other2.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.496
r_sphericity_free32.026
r_dihedral_angle_4_deg17.637
r_dihedral_angle_3_deg12.032
r_sphericity_bonded9.16
r_dihedral_angle_1_deg6.943
r_rigid_bond_restr3.985
r_long_range_B_refined3.734
r_long_range_B_other3.733
r_scangle_other2.223
r_scbond_it1.733
r_scbond_other1.732
r_angle_refined_deg1.566
r_mcangle_other1.349
r_mcangle_it1.279
r_angle_other_deg1.12
r_mcbond_it0.889
r_mcbond_other0.878
r_chiral_restr0.098
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.003
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 AtomsNumber
Protein Atoms2055
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing