3M5E

Crystal structure of human carbonic anhydrase isozyme II with 4-{[N-(6-chloro-5-formyl-2-methylthiopyrimidin-4-yl)amino]methyl}benzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M Na-bicine pH 9.0, 2M Na-malonate pH 7.55, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.141.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.423α = 90
b = 41.486β = 104.49
c = 72.434γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmBent, vertically focussing mirror2009-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8120EMBL/DESY, HAMBURGX13

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
11.741.4871000.0540.05432.811.6271162711613.3
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)
1.71.791000.1170.117137.83922

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 3HLJ1.740.127090272799.950.167520.163660.20202RANDOM12.678
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]
0.04-0.09-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.981
r_dihedral_angle_4_deg21.165
r_dihedral_angle_3_deg12.803
r_dihedral_angle_1_deg6.156
r_scangle_it2.923
r_scbond_it1.971
r_angle_refined_deg1.304
r_mcangle_it1.255
r_mcbond_it0.773
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.981
r_dihedral_angle_4_deg21.165
r_dihedral_angle_3_deg12.803
r_dihedral_angle_1_deg6.156
r_scangle_it2.923
r_scbond_it1.971
r_angle_refined_deg1.304
r_mcangle_it1.255
r_mcbond_it0.773
r_nbtor_refined0.309
r_nbd_refined0.194
r_symmetry_vdw_refined0.176
r_symmetry_hbond_refined0.147
r_xyhbond_nbd_refined0.132
r_chiral_restr0.092
r_metal_ion_refined0.049
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
Omodel building