3MHO

Crystal structure of human carbonic anhydrase isozyme II with 4-[N-(6-chloro-5-formyl-2-methylthiopyrimidin-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 DIFFUSION92930.1M Na-bicine pH 9, 2M Na-malonate pH 7, 0.2M ammonium sulfate , VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.13α = 90
b = 41.211β = 104.3
c = 72.076γ = 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 mirror2007-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.81EMBL/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
11.1541.21199.90.0660.06620.36.785279851948.522
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)
1.151.2199.70.3230.3234.16.112339

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 2NNO1.1540.838517585175856299.910.1770.1770.1760.192RANDOM11.419
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]
0.160.06-0.310.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.051
r_dihedral_angle_4_deg19.939
r_dihedral_angle_3_deg10.577
r_dihedral_angle_1_deg6.175
r_sphericity_free2.264
r_sphericity_bonded2.132
r_scangle_it2.021
r_scbond_it1.374
r_angle_refined_deg1.182
r_mcangle_it1.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.051
r_dihedral_angle_4_deg19.939
r_dihedral_angle_3_deg10.577
r_dihedral_angle_1_deg6.175
r_sphericity_free2.264
r_sphericity_bonded2.132
r_scangle_it2.021
r_scbond_it1.374
r_angle_refined_deg1.182
r_mcangle_it1.066
r_rigid_bond_restr0.873
r_mcbond_it0.63
r_nbtor_refined0.309
r_nbd_refined0.204
r_symmetry_vdw_refined0.156
r_xyhbond_nbd_refined0.104
r_symmetry_hbond_refined0.096
r_metal_ion_refined0.085
r_chiral_restr0.082
r_bond_refined_d0.006
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2039
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms47

Software

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