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Crystal structure of human carbonic anhydrase II in complex with Benzoxaborole at pH 7.4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 2.4 M SODIUM MALONATE
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.234 α = 90 b = 41.104 β = 103.92 c = 71.831 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944 2015-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.36 69.72 97.4 0.05 24.6 3.7 50126
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.38 79.1 0.292 2.3 2013
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1CA2 1.36 69.72 46386 2442 94.82 0.1232 0.121 0.1217 0.1647 0.164 RANDOM 14.163
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] 0.06 -0.7 -0.25 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.468 r_sphericity_free 27.566 r_dihedral_angle_4_deg 21.035 r_sphericity_bonded 13.278 r_dihedral_angle_3_deg 11.321 r_dihedral_angle_1_deg 6.944 r_rigid_bond_restr 3.745 r_mcangle_it 2.772 r_angle_refined_deg 2.277 r_mcbond_it 2.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.468 r_sphericity_free 27.566 r_dihedral_angle_4_deg 21.035 r_sphericity_bonded 13.278 r_dihedral_angle_3_deg 11.321 r_dihedral_angle_1_deg 6.944 r_rigid_bond_restr 3.745 r_mcangle_it 2.772 r_angle_refined_deg 2.277 r_mcbond_it 2.268 r_mcbond_other 2.254 r_angle_other_deg 1.065 r_chiral_restr 0.352 r_gen_planes_other 0.032 r_bond_other_d 0.022 r_bond_refined_d 0.018 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2073 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction CrystalClear data reduction REFMAC phasing