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Ni- Carbonic Anhydrase II pH 7.8 20 atm CO2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 1.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.1 41.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.395 α = 90 b = 41.365 β = 104.014 c = 72.127 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 ADSC QUANTUM 270 2019-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
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 1.2 30 95.4 0.072 0.077 0.028 0.995 23.1 7.6 72523
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 1.2 1.22 92.1 0.377 0.405 0.148 0.939 7.2 7.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5YUK 1.2 30 72507 3718 95.365 0.114 0.1124 0.1126 0.138 0.138 11.027
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] -0.038 0.075 -0.114 0.102
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.52 r_dihedral_angle_2_deg 34.724 r_dihedral_angle_4_deg 23.817 r_sphericity_bonded 13.173 r_dihedral_angle_3_deg 11.356 r_dihedral_angle_1_deg 7.188 r_rigid_bond_restr 6.22 r_lrange_it 5.134 r_lrange_other 4.046 r_scangle_other 3.544
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.52 r_dihedral_angle_2_deg 34.724 r_dihedral_angle_4_deg 23.817 r_sphericity_bonded 13.173 r_dihedral_angle_3_deg 11.356 r_dihedral_angle_1_deg 7.188 r_rigid_bond_restr 6.22 r_lrange_it 5.134 r_lrange_other 4.046 r_scangle_other 3.544 r_scangle_it 3.542 r_scbond_other 2.993 r_scbond_it 2.989 r_mcangle_other 2.639 r_mcangle_it 2.63 r_angle_refined_deg 2.382 r_mcbond_it 2.101 r_mcbond_other 1.814 r_angle_other_deg 1.208 r_symmetry_nbd_refined 0.321 r_nbd_refined 0.293 r_nbd_other 0.26 r_metal_ion_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.198 r_chiral_restr 0.192 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.14 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.029 r_gen_planes_refined 0.015 r_symmetry_xyhbond_nbd_other 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing