3M40

Crystal structure of human carbonic anhydrase isozyme II with 4-[N-(6-chloro-5-nitropyrimidin-4-yl)amino]benzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NNOPDB ENTRY 2NNO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M Na-bicine pH 9.0, 2M Na-Malonate pH7.55, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0840.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.184α = 90
b = 41.165β = 104.54
c = 72.477γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANELBent, vertically focussing mirror2008-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8150EMBL/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
11.616.29594.40.1610.16110.25.9319293014112.747
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)
1.61.6990.20.2020.2026.45.94203

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2NNO1.614.383012630126304794.10.160730.153590.22378RANDOM13.991
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]
-0.07-0.18-0.480.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.695
r_dihedral_angle_4_deg21.894
r_sphericity_free14.807
r_dihedral_angle_3_deg13.955
r_sphericity_bonded8.866
r_dihedral_angle_1_deg6.745
r_scangle_it6.057
r_scbond_it4.919
r_mcangle_it3.265
r_rigid_bond_restr3.027
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.695
r_dihedral_angle_4_deg21.894
r_sphericity_free14.807
r_dihedral_angle_3_deg13.955
r_sphericity_bonded8.866
r_dihedral_angle_1_deg6.745
r_scangle_it6.057
r_scbond_it4.919
r_mcangle_it3.265
r_rigid_bond_restr3.027
r_mcbond_it2.366
r_angle_refined_deg1.947
r_nbtor_refined0.312
r_nbd_refined0.231
r_symmetry_vdw_refined0.221
r_symmetry_hbond_refined0.163
r_chiral_restr0.148
r_xyhbond_nbd_refined0.148
r_metal_ion_refined0.041
r_bond_refined_d0.026
r_gen_planes_refined0.012
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing