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Crystal structure of the gamma carbonic anhydrase from Porphyromonas gingivalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q7MV79-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 2.0 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 2% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 3.07 59.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.752 α = 90 b = 120.752 β = 90 c = 91.31 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2024-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
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 2.4 45.37 95.9 0.13 0.139 0.049 0.999 18.5 15.3 28525
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 2.4 2.49 100 0.77 0.823 0.289 0.928 4.4 15.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 2.4 45.37 28494 1452 95.917 0.167 0.1654 0.1753 0.1965 0.1991 38.701
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] 0.553 0.277 0.553 -1.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.79 r_dihedral_angle_3_deg 17.895 r_dihedral_angle_4_deg 15.284 r_lrange_it 10.346 r_lrange_other 10.336 r_scangle_it 8.068 r_scangle_other 8.067 r_dihedral_angle_1_deg 7.855 r_mcangle_it 5.419 r_mcangle_other 5.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.79 r_dihedral_angle_3_deg 17.895 r_dihedral_angle_4_deg 15.284 r_lrange_it 10.346 r_lrange_other 10.336 r_scangle_it 8.068 r_scangle_other 8.067 r_dihedral_angle_1_deg 7.855 r_mcangle_it 5.419 r_mcangle_other 5.418 r_scbond_it 5.361 r_scbond_other 5.361 r_mcbond_it 3.737 r_mcbond_other 3.736 r_angle_refined_deg 1.77 r_angle_other_deg 1.327 r_symmetry_nbd_refined 0.275 r_nbd_other 0.232 r_symmetry_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.194 r_nbd_refined 0.186 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.141 r_metal_ion_refined 0.089 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3925 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing