3MHL

Crystal structure of human carbonic anhydrase isozyme II with 4-{[N-(6-methoxy-5-nitropyrimidin-4-yl)amino]methyl}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, 2.6M Na-malonate pH 7, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9938.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.712α = 90
b = 40.677β = 104.13
c = 70.716γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDVertically focussing mirror2009-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.9720EMBL/DESY, HAMBURGX12

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
11.940.6891000.0760.07637.915.3183881838824.1
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)
1.921000.2520.2527.511.52642

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 2NNO1.940.46183771837718491000.1680.1680.1620.219RANDOM25.533
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]
-0.31-0.71-1.431.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.629
r_dihedral_angle_3_deg15.689
r_dihedral_angle_4_deg15.074
r_dihedral_angle_1_deg7.2
r_scangle_it4.994
r_scbond_it3.528
r_mcangle_it2.219
r_angle_refined_deg1.998
r_mcbond_it1.483
r_chiral_restr0.345
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.629
r_dihedral_angle_3_deg15.689
r_dihedral_angle_4_deg15.074
r_dihedral_angle_1_deg7.2
r_scangle_it4.994
r_scbond_it3.528
r_mcangle_it2.219
r_angle_refined_deg1.998
r_mcbond_it1.483
r_chiral_restr0.345
r_nbtor_refined0.321
r_symmetry_hbond_refined0.231
r_nbd_refined0.207
r_symmetry_vdw_refined0.192
r_xyhbond_nbd_refined0.15
r_metal_ion_refined0.07
r_bond_refined_d0.023
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms32

Software

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