9FPT | pdb_00009fpt

Crystal structure of carbonic anhydrase II with methyl 4-chloro-3-sulfamoyl-benzoate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.1M sodium bicine (pH 9) and 2M sodium malonate (pH 7)
Crystal Properties
Matthews coefficientSolvent content
238

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.126α = 90
b = 40.928β = 103.99
c = 71.71γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.979700PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.1869.5896.70.0410.050.0190.99916.96.875321
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.181.24940.3840.4560.1730.9396.7

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 REPLACEMENTTHROUGHOUT1.1869.5867660762596.370.147050.14390.14920.175160.1764RANDOM22.688
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]
-0.350.9-0.640.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.291
r_rigid_bond_restr31.44
r_sphericity_free27.684
r_sphericity_bonded22.116
r_dihedral_angle_4_deg21.218
r_dihedral_angle_3_deg12.332
r_scbond_it8.672
r_dihedral_angle_1_deg7.186
r_mcangle_it6.496
r_long_range_B_refined6.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.291
r_rigid_bond_restr31.44
r_sphericity_free27.684
r_sphericity_bonded22.116
r_dihedral_angle_4_deg21.218
r_dihedral_angle_3_deg12.332
r_scbond_it8.672
r_dihedral_angle_1_deg7.186
r_mcangle_it6.496
r_long_range_B_refined6.464
r_mcbond_it5.757
r_angle_refined_deg2.131
r_chiral_restr0.403
r_bond_refined_d0.016
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 Atoms2038
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction
Cootmodel building
MOLREPphasing