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Crystal structure of a phosphocoumarin derivative in complex with human carbonic anhydrase II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EQU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.3 M sodium citrate, 0.1 M Tris-HCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.472 α = 90 b = 41.509 β = 104.23 c = 72.008 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 PIXEL DECTRIS PILATUS 6M 2025-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 ELETTRA 11.2C
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.65 50 100 0.111 0.121 0.048 0.999 8.1 6.2 29354
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) Redundancy Number Unique Reflections (All) 1 1.65 1.68 100 0.697 0.76 0.3 0.759 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.65 41.2 27573 1768 99.7 0.15293 0.15166 0.1656 0.17179 0.1843 RANDOM 19.13
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] 0.15 0.13 -0.58 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.001 r_dihedral_angle_1_deg 7.073 r_long_range_B_refined 6.033 r_long_range_B_other 6.021 r_dihedral_angle_2_deg 5.985 r_scangle_other 5.521 r_scbond_it 3.602 r_scbond_other 3.601 r_mcangle_it 2.613 r_mcangle_other 2.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.001 r_dihedral_angle_1_deg 7.073 r_long_range_B_refined 6.033 r_long_range_B_other 6.021 r_dihedral_angle_2_deg 5.985 r_scangle_other 5.521 r_scbond_it 3.602 r_scbond_other 3.601 r_mcangle_it 2.613 r_mcangle_other 2.613 r_mcbond_it 1.813 r_mcbond_other 1.813 r_angle_refined_deg 1.651 r_angle_other_deg 0.567 r_chiral_restr 0.083 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2039 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data reduction REFMAC phasing