4HT0

Crystal structure of human carbonic anhydrase isozyme II with the inhibitor.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HLJPDB ENTRY 3HLJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72910.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.140

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.018α = 90
b = 40.898β = 104.04
c = 71.604γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANELDetector swing-out angle up to 30 degrees2011-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.815EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.619.896.50.0610.06121.87.53022214.734
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.69970.1230.1235.37.84428

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB ENTRY 3HLJ1.619.83022230208303296.170.1720.1720.1680.21RANDOM15.521
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]
0.48-0.06-0.730.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.977
r_dihedral_angle_4_deg23.32
r_dihedral_angle_3_deg14.151
r_dihedral_angle_1_deg6.943
r_scangle_it4.578
r_scbond_it3.214
r_angle_refined_deg2.562
r_mcangle_it2.313
r_mcbond_it1.577
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.977
r_dihedral_angle_4_deg23.32
r_dihedral_angle_3_deg14.151
r_dihedral_angle_1_deg6.943
r_scangle_it4.578
r_scbond_it3.214
r_angle_refined_deg2.562
r_mcangle_it2.313
r_mcbond_it1.577
r_nbtor_refined0.318
r_chiral_restr0.272
r_nbd_refined0.231
r_symmetry_vdw_refined0.23
r_symmetry_hbond_refined0.213
r_xyhbond_nbd_refined0.164
r_metal_ion_refined0.056
r_bond_refined_d0.029
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOLREPphasing