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CO2 release in human carbonic anhydrase II crystals: reveal histidine 64 and solvent dynamics
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.3M sodium citrate, 100mM TrisHCl pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.08 40.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.258 α = 90 b = 41.294 β = 104.27 c = 72.094 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 210 2008-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.9795 CHESS F2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.25 50 98.8 0.055 34.3 6.8 62938
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 86 0.466 2.5 4
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 (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 THROUGHOUT 3D92 1.25 23.84 62938 3357 98.7 0.10128 0.09981 0.0992 0.12957 0.1286 RANDOM 16.137
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] 0.01 -0.01 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 51.052 r_dihedral_angle_2_deg 32.698 r_dihedral_angle_4_deg 26.582 r_sphericity_bonded 13.37 r_dihedral_angle_3_deg 11.445 r_dihedral_angle_1_deg 6.655 r_rigid_bond_restr 6.324 r_long_range_B_refined 5.985 r_long_range_B_other 5.253 r_scangle_other 3.922
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 51.052 r_dihedral_angle_2_deg 32.698 r_dihedral_angle_4_deg 26.582 r_sphericity_bonded 13.37 r_dihedral_angle_3_deg 11.445 r_dihedral_angle_1_deg 6.655 r_rigid_bond_restr 6.324 r_long_range_B_refined 5.985 r_long_range_B_other 5.253 r_scangle_other 3.922 r_scbond_it 3.817 r_scbond_other 3.817 r_mcangle_other 2.268 r_mcangle_it 2.254 r_angle_refined_deg 2.019 r_mcbond_it 1.753 r_mcbond_other 1.721 r_angle_other_deg 1.002 r_chiral_restr 0.161 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 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 310 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing