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Ni- Carbonic Anhydrase II pH 7.8 15 atm CO2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LV5
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 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.424 α = 90 b = 41.332 β = 104.01 c = 72.142 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 2020-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 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 0.06 0.064 0.023 0.998 33.7 7.5 72988
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 93.3 0.357 0.384 0.141 0.941 6.5 7.4
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 1.2 30 69386 3586 95.97 0.11193 0.11088 0.1108 0.13298 0.1329 RANDOM 11.81
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] -0.1 0.08 -0.15 0.18
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 49.762 r_dihedral_angle_2_deg 34.448 r_dihedral_angle_4_deg 23.969 r_sphericity_bonded 14.94 r_dihedral_angle_3_deg 11.464 r_dihedral_angle_1_deg 7.054 r_rigid_bond_restr 6.097 r_long_range_B_refined 5.671 r_long_range_B_other 4.522 r_scangle_other 3.631
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 49.762 r_dihedral_angle_2_deg 34.448 r_dihedral_angle_4_deg 23.969 r_sphericity_bonded 14.94 r_dihedral_angle_3_deg 11.464 r_dihedral_angle_1_deg 7.054 r_rigid_bond_restr 6.097 r_long_range_B_refined 5.671 r_long_range_B_other 4.522 r_scangle_other 3.631 r_mcangle_other 3.194 r_mcangle_it 3.178 r_scbond_it 2.912 r_scbond_other 2.91 r_mcbond_it 2.487 r_angle_refined_deg 2.39 r_mcbond_other 2.156 r_angle_other_deg 1.319 r_chiral_restr 0.2 r_bond_refined_d 0.03 r_gen_planes_refined 0.015 r_gen_planes_other 0.01 r_bond_other_d 0.002 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
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