3S9T | pdb_00003s9t

Crystal structure of human carbonic anhydrase isozyme II with 2-chloro-5-{[(4,6-dimethyl-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HLJPDB entry 3HLJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72982.4M Na-Malonate, pH 7, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.139.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.012α = 90
b = 41.058β = 104.15
c = 71.839γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMosaic, 225 mmDetector swing-out angle up to 30 degrees2010-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.9748EMBL/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
11.369.6731000.1290.1291475864210.8
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)
11.31.371000.3680.3681.65.88514

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRTHROUGHOUTPDB entry 3HLJ1.369.67586255862559081000.1480.1480.1430.140.1920.1893RANDOM14.204
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]
0.58-0.60.34-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.353
r_dihedral_angle_4_deg21.041
r_sphericity_free16.406
r_dihedral_angle_3_deg13.316
r_sphericity_bonded10.158
r_dihedral_angle_1_deg6.99
r_scangle_it6.921
r_scbond_it5.479
r_mcangle_it4.035
r_rigid_bond_restr3.716
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.353
r_dihedral_angle_4_deg21.041
r_sphericity_free16.406
r_dihedral_angle_3_deg13.316
r_sphericity_bonded10.158
r_dihedral_angle_1_deg6.99
r_scangle_it6.921
r_scbond_it5.479
r_mcangle_it4.035
r_rigid_bond_restr3.716
r_mcbond_it3.185
r_angle_refined_deg2.641
r_nbtor_refined0.321
r_nbd_refined0.24
r_symmetry_vdw_refined0.233
r_symmetry_hbond_refined0.232
r_chiral_restr0.203
r_xyhbond_nbd_refined0.186
r_metal_ion_refined0.061
r_bond_refined_d0.034
r_gen_planes_refined0.018
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection