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Crystal structure of the gamma-carbonic anhydrase from the polyextremophilic bacterium Aeribacillus pallidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.1 M Tris pH 7.5, 14% (w/v) polyethylene glycol 400, and 200 mM ZnSO4
Crystal Properties Matthews coefficient Solvent content 2.45 49.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.911 α = 90 b = 110.672 β = 118.8 c = 98.578 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS EIGER X 9M 2020-10-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.7 40.36 97.6 0.036 14.9 4.2 113523
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 0.189 47.4
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 FREE R-VALUE 6IVE 1.7 40.36 113523 5934 97.15 0.21475 0.21312 0.2046 0.24531 0.2251 RANDOM 20.247
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] 1.44 0.63 -0.56 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 15.268 r_dihedral_angle_3_deg 13.205 r_long_range_B_refined 7.243 r_dihedral_angle_1_deg 7.233 r_long_range_B_other 7.216 r_scangle_other 4.328 r_scbond_it 2.769 r_scbond_other 2.757 r_mcangle_it 2.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 15.268 r_dihedral_angle_3_deg 13.205 r_long_range_B_refined 7.243 r_dihedral_angle_1_deg 7.233 r_long_range_B_other 7.216 r_scangle_other 4.328 r_scbond_it 2.769 r_scbond_other 2.757 r_mcangle_it 2.409 r_mcangle_other 2.409 r_mcbond_it 1.682 r_mcbond_other 1.681 r_angle_refined_deg 1.566 r_angle_other_deg 1.322 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7938 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing