5G03

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 5A6H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5150 NL PROTEIN AT 5.5 MG/ML PLUS 120 NL RESERVOIR AND 30 NL SEEDS IN SITTING DROP PLATES. RESERVOIR WAS 2.6 TO 2.8 M AMMONIUM SULFATE PLUS 100 MM TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.0941.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.88α = 90
b = 41.28β = 104.11
c = 71.788γ = 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
11.3541.395.70.0719.17.650188
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)
11.351.3790.50.782.47.1

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 REPLACEMENTTHROUGHOUT5A6H1.3569.6247704246795.380.129090.12750.16005RANDOM15.29
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]
-0.090.030.18-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.53
r_sphericity_free30.807
r_dihedral_angle_4_deg19.113
r_dihedral_angle_3_deg12.126
r_sphericity_bonded9.084
r_dihedral_angle_1_deg6.572
r_rigid_bond_restr4.438
r_scbond_it2.669
r_angle_refined_deg1.862
r_mcangle_it1.704
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.53
r_sphericity_free30.807
r_dihedral_angle_4_deg19.113
r_dihedral_angle_3_deg12.126
r_sphericity_bonded9.084
r_dihedral_angle_1_deg6.572
r_rigid_bond_restr4.438
r_scbond_it2.669
r_angle_refined_deg1.862
r_mcangle_it1.704
r_mcbond_it1.342
r_mcbond_other1.334
r_angle_other_deg1.086
r_chiral_restr0.109
r_bond_refined_d0.013
r_gen_planes_refined0.01
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 Atoms261
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing