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Carbonic anhydrase II variant with bound iron complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M Na Acet, 0.1 M Na Cacod 6.5 pH, 30 %w/v PEG 8K
Crystal Properties Matthews coefficient Solvent content 2.06 40.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.344 α = 90 b = 70.664 β = 90 c = 146.349 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 XE 16M 2023-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.93 38.75 93.41 0.16 0.166 0.045 0.998 12.29 13.1 17297
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 1.93 1.999 85.81 1.303 1.358 0.376 0.711 2.07 12.3
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 FREE R-VALUE 1.93 38.75 16439 858 93.45 0.18354 0.18051 0.183 0.24122 0.243 RANDOM 28.399
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] 0.04 -0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.326 r_dihedral_angle_2_deg 11.37 r_dihedral_angle_1_deg 7.435 r_long_range_B_other 6.081 r_long_range_B_refined 6.068 r_scangle_other 4.993 r_scbond_it 3.354 r_scbond_other 3.344 r_mcangle_it 3.341 r_mcangle_other 3.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.326 r_dihedral_angle_2_deg 11.37 r_dihedral_angle_1_deg 7.435 r_long_range_B_other 6.081 r_long_range_B_refined 6.068 r_scangle_other 4.993 r_scbond_it 3.354 r_scbond_other 3.344 r_mcangle_it 3.341 r_mcangle_other 3.339 r_mcbond_it 2.499 r_mcbond_other 2.492 r_angle_refined_deg 1.81 r_angle_other_deg 0.587 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 2056 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing