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Human Carbonic Anhydrase II native 13 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, 100 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.08 40.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.172 α = 90 b = 41.32 β = 104.073 c = 71.993 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 2019-04-09 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) 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 1.15 30 99.4 0.049 33.05 6.6 84743
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.17 0.436 4.78
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 1.151 29.07 84726 4109 99.298 0.104 0.1028 0.103 0.1288 0.1288 16.179
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] -0.002 0.009 -0.007
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.661 r_dihedral_angle_2_deg 33.823 r_dihedral_angle_4_deg 20.853 r_dihedral_angle_3_deg 12.615 r_sphericity_bonded 12.302 r_rigid_bond_restr 6.957 r_dihedral_angle_1_deg 6.716 r_lrange_it 5.46 r_lrange_other 4.808 r_scangle_it 3.922
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.661 r_dihedral_angle_2_deg 33.823 r_dihedral_angle_4_deg 20.853 r_dihedral_angle_3_deg 12.615 r_sphericity_bonded 12.302 r_rigid_bond_restr 6.957 r_dihedral_angle_1_deg 6.716 r_lrange_it 5.46 r_lrange_other 4.808 r_scangle_it 3.922 r_scangle_other 3.921 r_scbond_it 3.434 r_scbond_other 3.434 r_mcangle_other 2.666 r_mcangle_it 2.639 r_angle_refined_deg 2.455 r_mcbond_it 2.035 r_mcbond_other 1.84 r_angle_other_deg 1.729 r_nbd_other 0.341 r_symmetry_nbd_refined 0.31 r_nbd_refined 0.298 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.186 r_chiral_restr 0.165 r_symmetry_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_refined 0.124 r_symmetry_nbtor_other 0.079 r_metal_ion_refined 0.066 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 r_gen_planes_other 0.013 r_symmetry_xyhbond_nbd_other 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing