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Ni- Carbonic Anhydrase II pH 11.0 0 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 11 293 1.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.09 41.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.522 α = 90 b = 41.23 β = 104.055 c = 71.873 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 97.5 0.085 0.092 0.034 0.99 23.1 7.4 73833
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 94.7 0.297 0.32 0.118 0.956 8.4 7.3
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 73791 3781 97.45 0.118 0.1171 0.1172 0.1394 0.1396 12.257
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] -0.122 0.015 -0.018 0.117
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.17 r_dihedral_angle_2_deg 34.609 r_dihedral_angle_4_deg 25.967 r_sphericity_bonded 12.668 r_dihedral_angle_3_deg 12.664 r_dihedral_angle_1_deg 6.66 r_rigid_bond_restr 6.481 r_lrange_it 5.349 r_lrange_other 4.441 r_scangle_it 4.091
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.17 r_dihedral_angle_2_deg 34.609 r_dihedral_angle_4_deg 25.967 r_sphericity_bonded 12.668 r_dihedral_angle_3_deg 12.664 r_dihedral_angle_1_deg 6.66 r_rigid_bond_restr 6.481 r_lrange_it 5.349 r_lrange_other 4.441 r_scangle_it 4.091 r_scangle_other 4.09 r_scbond_other 3.355 r_scbond_it 3.354 r_angle_refined_deg 2.552 r_mcangle_other 2.056 r_mcangle_it 2.016 r_mcbond_it 1.573 r_mcbond_other 1.372 r_angle_other_deg 1.272 r_symmetry_nbd_refined 0.331 r_nbd_refined 0.294 r_nbd_other 0.291 r_symmetry_xyhbond_nbd_refined 0.216 r_chiral_restr 0.205 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.147 r_metal_ion_refined 0.139 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.03 r_gen_planes_refined 0.015 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 279 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing