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Zn-Carbonic Anhydrase II complexed with 3NPA under 15 atm CO2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9KIB
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 2.07 40.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.971 α = 90 b = 41.275 β = 104.06 c = 72.041 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 PIXEL DECTRIS EIGER X 9M 2019-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.8856 PAL/PLS 5C (4A)
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 1.14 30 95.1 0.046 0.05 0.019 1 41.6 6.8 83043
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 1.14 1.16 92.4 0.305 0.331 0.125 0.941 6.7 6.8
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 1.14 30 78972 4022 95.01 0.12206 0.12058 0.1209 0.15243 0.153 RANDOM 14.975
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] 0.48 -0.28 -0.09 -0.22
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 59.292 r_dihedral_angle_2_deg 33.573 r_dihedral_angle_4_deg 21.398 r_sphericity_bonded 17.52 r_dihedral_angle_3_deg 12.264 r_long_range_B_refined 8.53 r_long_range_B_other 7.221 r_rigid_bond_restr 7.166 r_dihedral_angle_1_deg 7.1 r_scangle_other 4.038
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 59.292 r_dihedral_angle_2_deg 33.573 r_dihedral_angle_4_deg 21.398 r_sphericity_bonded 17.52 r_dihedral_angle_3_deg 12.264 r_long_range_B_refined 8.53 r_long_range_B_other 7.221 r_rigid_bond_restr 7.166 r_dihedral_angle_1_deg 7.1 r_scangle_other 4.038 r_scbond_it 3.614 r_scbond_other 3.613 r_mcangle_other 3.247 r_mcangle_it 3.218 r_angle_refined_deg 2.738 r_mcbond_it 2.56 r_mcbond_other 2.535 r_angle_other_deg 1.968 r_chiral_restr 0.18 r_bond_refined_d 0.032 r_gen_planes_other 0.024 r_gen_planes_refined 0.017 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 354 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing