5G0B

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 DROPS WITH 150 NL PROTEIN AT 5.5 MG/ML WITH 120 NL RESERVOIR AND 30 NL SEEDS. THE RESERVOIR HAD 2.6 TO 2.8 M AMMONIUM SULFATE WITH 100 MM TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.0941.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.706α = 90
b = 41.286β = 104.19
c = 72.13γ = 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
11.5541.3980.0815.87.534094
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)
11.551.5895.70.722.67.2

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 5A6H1.5569.9332405167597.730.134730.132480.17851RANDOM16.503
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]
-0.370.41-0.320.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.407
r_sphericity_free21.591
r_dihedral_angle_4_deg17.521
r_dihedral_angle_3_deg12.446
r_dihedral_angle_1_deg6.809
r_sphericity_bonded5.844
r_rigid_bond_restr2.074
r_angle_refined_deg1.658
r_scbond_it1.572
r_mcangle_it1.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.407
r_sphericity_free21.591
r_dihedral_angle_4_deg17.521
r_dihedral_angle_3_deg12.446
r_dihedral_angle_1_deg6.809
r_sphericity_bonded5.844
r_rigid_bond_restr2.074
r_angle_refined_deg1.658
r_scbond_it1.572
r_mcangle_it1.306
r_mcbond_it1.102
r_mcbond_other1.074
r_angle_other_deg0.988
r_chiral_restr0.101
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.004
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2045
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing