3M3X

Crystal structure of human carbonic anhydrase isozyme II with 4-{2-[N-(6-methoxy-5-nitropyrimidin-4-yl)amino]ethyl}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 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.035α = 90
b = 41.051β = 104.39
c = 71.805γ = 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 mirror2009-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8120EMBL/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
11.6841.0798.30.0390.03950.511.2272112674916.2
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)
1.681.7797.60.0790.07917.87.63813

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 2NNO1.6831.862721126728265297.950.168450.162680.22167RANDOM16.154
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]
0.20.11-0.570.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.602
r_dihedral_angle_4_deg20.855
r_dihedral_angle_3_deg14.54
r_dihedral_angle_1_deg7.035
r_scangle_it4.633
r_scbond_it3.123
r_mcangle_it2.208
r_angle_refined_deg2.187
r_mcbond_it1.471
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.602
r_dihedral_angle_4_deg20.855
r_dihedral_angle_3_deg14.54
r_dihedral_angle_1_deg7.035
r_scangle_it4.633
r_scbond_it3.123
r_mcangle_it2.208
r_angle_refined_deg2.187
r_mcbond_it1.471
r_nbtor_refined0.314
r_symmetry_vdw_refined0.252
r_nbd_refined0.233
r_symmetry_hbond_refined0.194
r_xyhbond_nbd_refined0.17
r_chiral_restr0.166
r_metal_ion_refined0.082
r_bond_refined_d0.027
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms29

Software

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