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Human carbonic anhydrase I covalently bound to AV21-08
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 291 TrisHCl pH8.5 0.1M, NaCl 0.2M, PEG3350 28% (w/v)
Crystal Properties Matthews coefficient Solvent content 2.42 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.415 α = 90 b = 73.265 β = 90 c = 120.57 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2023-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97552 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.39 120.57 98.3 0.053 0.057 0.022 1 13.8 13 110929 22.1
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 1.39 1.41 67.6 2.677 2.984 1.266 0.214 0.5 4.7
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 MOLECULAR REPLACEMENT THROUGHOUT 1.39 62.61 99219 10962 98.1 0.205 0.202 0.2041 0.234 0.2418 RANDOM 26.61
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] -0.28 1.85 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.601 r_dihedral_angle_4_deg 19.264 r_dihedral_angle_3_deg 13.153 r_dihedral_angle_1_deg 7.314 r_long_range_B_refined 5.466 r_scbond_it 3.121 r_mcangle_it 2.806 r_mcbond_it 2.052 r_angle_refined_deg 1.854 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.601 r_dihedral_angle_4_deg 19.264 r_dihedral_angle_3_deg 13.153 r_dihedral_angle_1_deg 7.314 r_long_range_B_refined 5.466 r_scbond_it 3.121 r_mcangle_it 2.806 r_mcbond_it 2.052 r_angle_refined_deg 1.854 r_chiral_restr 0.122 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4020 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing