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human carbonic anhydrase II in complex with 4-(((dimethoxyphosphoryl)(4-((dimethoxyphosphoryl)((4-sulfamoylphenyl)amino)methyl)phenyl)methyl)amino)phenyl sulfuramidite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.12 42.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.555 α = 90 b = 41.636 β = 104.467 c = 72.519 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 2023-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.25 41.24 95.8 0.047 0.052 0.999 18.6 5.7 65314
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 64.8 0.382 0.45 0.868 2.8 3.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1.25 41.24 65097 3164 95.421 0.139 0.1371 0.1449 0.1704 0.1772 16.472
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] 1.749 -0.221 -0.096 -1.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.84 r_dihedral_angle_4_deg 23.403 r_dihedral_angle_3_deg 13.251 r_rigid_bond_restr 8.916 r_scangle_it 8.725 r_scangle_other 8.723 r_lrange_it 7.938 r_lrange_other 7.937 r_mcbond_other 7.785 r_mcbond_it 7.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.84 r_dihedral_angle_4_deg 23.403 r_dihedral_angle_3_deg 13.251 r_rigid_bond_restr 8.916 r_scangle_it 8.725 r_scangle_other 8.723 r_lrange_it 7.938 r_lrange_other 7.937 r_mcbond_other 7.785 r_mcbond_it 7.783 r_mcangle_other 7.622 r_mcangle_it 7.62 r_dihedral_angle_1_deg 6.94 r_scbond_it 6.558 r_scbond_other 6.556 r_angle_refined_deg 2.119 r_angle_other_deg 1.56 r_symmetry_nbd_refined 0.274 r_nbd_refined 0.235 r_nbd_other 0.211 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.129 r_symmetry_xyhbond_nbd_refined 0.112 r_metal_ion_refined 0.101 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2053 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing