3MHI

Crystal structure of human carbonic anhydrase isozyme II with 4-{[(5-nitro-6-oxo-1,6-dihydro-4-pyrimidinyl)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 DIFFUSION92930.1M Na-bicine pH 9, 2.6M Na-malonate pH 7, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.242α = 90
b = 41.24β = 104.43
c = 71.95γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic mirrors2010-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.721.10199.90.0450.04531.29.4267202663916
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)
1.71.7999.30.1850.18510.78.83843

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 3HLJ1.721.12662826628267899.890.1670.1670.1620.215RANDOM14.065
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]
0.18-0.03-0.01-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.407
r_dihedral_angle_4_deg20.531
r_dihedral_angle_3_deg13.358
r_dihedral_angle_1_deg6.865
r_scangle_it4.848
r_scbond_it3.258
r_angle_refined_deg2.234
r_mcangle_it2.204
r_mcbond_it1.467
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.407
r_dihedral_angle_4_deg20.531
r_dihedral_angle_3_deg13.358
r_dihedral_angle_1_deg6.865
r_scangle_it4.848
r_scbond_it3.258
r_angle_refined_deg2.234
r_mcangle_it2.204
r_mcbond_it1.467
r_nbtor_refined0.309
r_symmetry_vdw_refined0.251
r_nbd_refined0.221
r_symmetry_hbond_refined0.195
r_chiral_restr0.171
r_xyhbond_nbd_refined0.162
r_metal_ion_refined0.052
r_bond_refined_d0.029
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms53

Software

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