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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 1.3 M sodium citrate, 100 mM TrisHCl pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.07 40.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.22 α = 90 b = 41.244 β = 104.19 c = 71.963 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 1.45 50 100 0.077 28.5 7.4 40706
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 1.45 1.48 100 0.438 3.9 7.3
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 1.45 24.52 40706 2161 99.85 0.0986 0.09654 0.0963 0.13641 0.1365 RANDOM 17.984
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
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.499 r_dihedral_angle_2_deg 32.984 r_dihedral_angle_4_deg 25.458 r_sphericity_bonded 12.213 r_dihedral_angle_3_deg 11.642 r_dihedral_angle_1_deg 6.61 r_rigid_bond_restr 5.372 r_long_range_B_refined 5.346 r_long_range_B_other 4.613 r_scangle_other 4.007
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.499 r_dihedral_angle_2_deg 32.984 r_dihedral_angle_4_deg 25.458 r_sphericity_bonded 12.213 r_dihedral_angle_3_deg 11.642 r_dihedral_angle_1_deg 6.61 r_rigid_bond_restr 5.372 r_long_range_B_refined 5.346 r_long_range_B_other 4.613 r_scangle_other 4.007 r_scbond_it 3.739 r_scbond_other 3.739 r_mcangle_other 2.393 r_mcangle_it 2.381 r_mcbond_it 1.977 r_mcbond_other 1.977 r_angle_refined_deg 1.87 r_angle_other_deg 0.95 r_chiral_restr 0.141 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 271 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing