3MHM

Crystal structure of human carbonic anhydrase isozyme II with 4-{[N-(6-benzylamino-5-nitropyrimidin-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 DIFFUSION82930.1M Na-bicine pH 9, 0.2M ammonium sulfate, 2.4M Na-malonate pH 7, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0840.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.25α = 90
b = 41.171β = 104.1
c = 72.243γ = 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 mirror2009-12-18MSINGLE 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
11.570.06897.30.0330.03325.44.1387633771614.2
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)
1.51.5896.10.1570.1575.83.95409

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 3HLJ1.539.863886837698376096.990.137270.131790.18657RANDOM15.4
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]
0.010.040.19-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.961
r_dihedral_angle_4_deg23.372
r_dihedral_angle_3_deg13.835
r_sphericity_free12.994
r_sphericity_bonded8.281
r_dihedral_angle_1_deg7.139
r_scangle_it6.072
r_scbond_it4.607
r_mcangle_it3.483
r_rigid_bond_restr2.857
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.961
r_dihedral_angle_4_deg23.372
r_dihedral_angle_3_deg13.835
r_sphericity_free12.994
r_sphericity_bonded8.281
r_dihedral_angle_1_deg7.139
r_scangle_it6.072
r_scbond_it4.607
r_mcangle_it3.483
r_rigid_bond_restr2.857
r_mcbond_it2.568
r_angle_refined_deg2.158
r_nbtor_refined0.311
r_symmetry_hbond_refined0.259
r_symmetry_vdw_refined0.247
r_nbd_refined0.232
r_chiral_restr0.163
r_xyhbond_nbd_refined0.147
r_metal_ion_refined0.079
r_bond_refined_d0.028
r_gen_planes_refined0.013
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 Atoms2049
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms34

Software

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