4E3D

Nucleophile recognition as an alternative inhibition mode for benzoic acid based carbonic anhydrase inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KS3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82913M Ammonium Sulfate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0941.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.204α = 90
b = 41.479β = 104.32
c = 72.119γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002011-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5711.54184

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.669.8899.66321423203211
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.64298.84

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KS31.669.8813203232032162899.660.1710.171020.168870.21076RANDOM10.422
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]
-0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.01
r_dihedral_angle_4_deg22.302
r_dihedral_angle_3_deg13.127
r_dihedral_angle_1_deg6.961
r_scangle_it4.781
r_scbond_it3.16
r_mcangle_it2.136
r_angle_refined_deg2.103
r_mcbond_it1.339
r_chiral_restr0.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.01
r_dihedral_angle_4_deg22.302
r_dihedral_angle_3_deg13.127
r_dihedral_angle_1_deg6.961
r_scangle_it4.781
r_scbond_it3.16
r_mcangle_it2.136
r_angle_refined_deg2.103
r_mcbond_it1.339
r_chiral_restr0.157
r_bond_refined_d0.025
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms39

Software

Software
Software NamePurpose
APEXdata collection
PHASERphasing
REFMACrefinement
APEXdata reduction