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Ni- Carbonic Anhydrase II pH 11.0 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 11 293 1.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.1 41.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.419 α = 90 b = 41.398 β = 104.04 c = 72.191 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 96.1 0.047 0.051 0.019 0.998 40.6 7.5 73282
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 93 0.227 0.244 0.09 0.975 10.1 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 73217 3748 96.09 0.113 0.1121 0.1121 0.1364 0.1366 11.329
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] -0.121 -0.024 0.019 0.101
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 50.339 r_dihedral_angle_2_deg 34.886 r_dihedral_angle_4_deg 23.356 r_sphericity_bonded 12.299 r_dihedral_angle_3_deg 11.544 r_dihedral_angle_1_deg 7.032 r_rigid_bond_restr 6.084 r_lrange_it 4.717 r_lrange_other 3.981 r_scangle_other 3.854
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 50.339 r_dihedral_angle_2_deg 34.886 r_dihedral_angle_4_deg 23.356 r_sphericity_bonded 12.299 r_dihedral_angle_3_deg 11.544 r_dihedral_angle_1_deg 7.032 r_rigid_bond_restr 6.084 r_lrange_it 4.717 r_lrange_other 3.981 r_scangle_other 3.854 r_scangle_it 3.852 r_mcangle_other 3.546 r_mcangle_it 3.521 r_mcbond_it 3.064 r_scbond_other 2.869 r_scbond_it 2.866 r_angle_refined_deg 2.352 r_mcbond_other 2.033 r_angle_other_deg 1.247 r_symmetry_nbd_refined 0.308 r_nbd_other 0.3 r_nbd_refined 0.29 r_symmetry_xyhbond_nbd_refined 0.231 r_symmetry_nbd_other 0.203 r_chiral_restr 0.194 r_nbtor_refined 0.185 r_metal_ion_refined 0.177 r_xyhbond_nbd_refined 0.138 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_symmetry_xyhbond_nbd_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing