3PYK

Human Carbonic Anhydrase II as Host for Pianostool Complexes Bearing a Sulfonamide Anchor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CBAPDB entry 2cba

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82773 uL protein solution (20 mg/mL lyophilized hCAII in 50 mM Tris-sulfate, 1 mM methyl mercuric acetate) and 5 uL precipitating buffer (2.6 M ammonium sulfate, 50 mM Tris-sulfate were mixed and equilibrated against 500 uL precipitating buffer. Single crystals were transferred into a cross-linking buffer, which was prepared from 10 uL precipitating buffer and 5 uL glutaraldehyde solution (0.8 % glutaraldehyde, 4 M ammonium sulfate, 50 mM Tris-sulfate) and equilibrated for 18 h. Cross-linked crystals were transferred into soaking buffer (9 uL precipitating buffer, 0.5 uL 60 mM {(6-benzene)Ru(bispy 3)Cl}+ in DMSO) and equilibrated for 54 h, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0941.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.099α = 90
b = 41.493β = 104.33
c = 72.382γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER1.0

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
11.330.696.95900722
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)
11.31.33491.20.3092.82.7

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 2cba1.330.659007298498.740.129470.127560.16471RANDOM12.373
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]
-0.04-0.280.15-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.962
r_dihedral_angle_4_deg17.319
r_dihedral_angle_3_deg12.195
r_scangle_it8.349
r_dihedral_angle_1_deg6.622
r_scbond_it6.395
r_mcangle_it4.386
r_mcbond_it3.195
r_rigid_bond_restr2.895
r_angle_refined_deg1.454
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.962
r_dihedral_angle_4_deg17.319
r_dihedral_angle_3_deg12.195
r_scangle_it8.349
r_dihedral_angle_1_deg6.622
r_scbond_it6.395
r_mcangle_it4.386
r_mcbond_it3.195
r_rigid_bond_restr2.895
r_angle_refined_deg1.454
r_mcbond_other1.233
r_angle_other_deg0.87
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2058
Nucleic Acid Atoms
Solvent Atoms420
Heterogen Atoms48

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling