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Three dimensional structure of human carbonic anhydrase XII in complex with sulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, PH 5.6, 31% PEG 4000, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS DISSOLVED IN 100% DMSO), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.11 41.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.78 α = 81.47 b = 67.48 β = 84.09 c = 81 γ = 86.45
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 2019-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.68 79.74 85.5 0.164 4.5 3.1 94857 9.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.77 85.4 0.561 2 3
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 THROUGHOUT 1.68 79.74 90109 4734 85.46 0.2022 0.19939 0.208 0.25406 0.2614 RANDOM 14.067
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] -1.39 -0.26 -0.05 0.45 0.02 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.773 r_dihedral_angle_3_deg 14.292 r_dihedral_angle_1_deg 7.627 r_long_range_B_refined 4.676 r_long_range_B_other 4.396 r_scangle_other 2.211 r_mcangle_it 1.89 r_mcangle_other 1.89 r_angle_refined_deg 1.488 r_scbond_it 1.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.773 r_dihedral_angle_3_deg 14.292 r_dihedral_angle_1_deg 7.627 r_long_range_B_refined 4.676 r_long_range_B_other 4.396 r_scangle_other 2.211 r_mcangle_it 1.89 r_mcangle_other 1.89 r_angle_refined_deg 1.488 r_scbond_it 1.384 r_scbond_other 1.384 r_mcbond_it 1.149 r_mcbond_other 1.148 r_angle_other_deg 0.503 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 8330 Nucleic Acid Atoms Solvent Atoms 1202 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement SCALA data scaling