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Zn-Carbonic Anhydrase II complexed with 3NPA at 140 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Y2A
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 2.06 40.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.911 α = 90 b = 41.155 β = 104.27 c = 72.232 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 140 CCD RAYONIX MX225-HS 2019-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6D 0.97934 PAL/PLS 6D
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 99.5 0.075 0.088 0.045 0.992 15.7 3.6 74230
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 96.3 0.31 0.378 0.212 0.86 3.5 2.8
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 1.2 30 70539 3675 99.47 0.1465 0.14486 0.1454 0.17935 0.1807 RANDOM 14.592
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] 0.49 -0.23 -0.05 -0.29
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.783 r_dihedral_angle_2_deg 35.229 r_dihedral_angle_4_deg 25.888 r_sphericity_bonded 15.551 r_dihedral_angle_3_deg 12.304 r_dihedral_angle_1_deg 7.024 r_scangle_other 5.744 r_long_range_B_refined 5.682 r_long_range_B_other 5.226 r_rigid_bond_restr 5.163
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.783 r_dihedral_angle_2_deg 35.229 r_dihedral_angle_4_deg 25.888 r_sphericity_bonded 15.551 r_dihedral_angle_3_deg 12.304 r_dihedral_angle_1_deg 7.024 r_scangle_other 5.744 r_long_range_B_refined 5.682 r_long_range_B_other 5.226 r_rigid_bond_restr 5.163 r_scbond_it 4.922 r_scbond_other 4.921 r_mcangle_other 2.658 r_mcangle_it 2.632 r_angle_refined_deg 2.56 r_mcbond_it 2.317 r_mcbond_other 2.299 r_angle_other_deg 1.228 r_chiral_restr 0.177 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 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 242 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing