8RJ2 | pdb_00008rj2

Crystal structure of carbonic anhydrase II with N-butyl-4-chloro-2-(cyclohexylsulfanyl)-5-sulfamoylbenzamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HT0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2910.1M sodium bicine (pH 9) and 2M sodium malonate (pH 7)
Crystal Properties
Matthews coefficientSolvent content
2.0138.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.067α = 90
b = 41.148β = 104.15
c = 72.028γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-01-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.975522PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.1240.7989.30.0460.0550.02125.16.981344
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.121.1860.40.1450.1750.0696.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.1240.7973141818888.940.151630.148930.14880.176010.1761RANDOM17.582
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]
0.530.08-0.41-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.891
r_rigid_bond_restr30.338
r_dihedral_angle_4_deg25.025
r_sphericity_free21.094
r_sphericity_bonded17.764
r_dihedral_angle_3_deg13.426
r_mcbond_it8.576
r_dihedral_angle_1_deg6.896
r_long_range_B_refined6.123
r_scbond_it5.498
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.891
r_rigid_bond_restr30.338
r_dihedral_angle_4_deg25.025
r_sphericity_free21.094
r_sphericity_bonded17.764
r_dihedral_angle_3_deg13.426
r_mcbond_it8.576
r_dihedral_angle_1_deg6.896
r_long_range_B_refined6.123
r_scbond_it5.498
r_mcangle_it5.425
r_angle_refined_deg2.272
r_chiral_restr0.135
r_bond_refined_d0.017
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2041
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
Cootmodel building