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Carbonic Anhydrase CAIX mimic in complex with inhibitor JS13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PO6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 291 protein 25 mg/mL, 1.6M sodium citrate, 50mM Tris H2SO4 pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.82 α = 90 b = 41.15 β = 103.81 c = 72.01 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 PIXEL DECTRIS PILATUS 300K 2017-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.35 40.61 79.1 0.03 0.035 1 28.17 3.704 41518 17.073
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.39 53.8 0.299 0.365 0.872 3.36 2.859
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 3PO6 1.35 40.61 40480 1038 79.1 0.11381 0.11277 0.1145 0.15376 0.1571 RANDOM 13.18
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] -0.05 -0.16 0.11 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.57 r_dihedral_angle_4_deg 19.334 r_sphericity_free 16.889 r_dihedral_angle_3_deg 11.507 r_dihedral_angle_1_deg 7.047 r_sphericity_bonded 6.963 r_rigid_bond_restr 2.867 r_long_range_B_refined 2.679 r_long_range_B_other 2.502 r_scangle_other 2.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.57 r_dihedral_angle_4_deg 19.334 r_sphericity_free 16.889 r_dihedral_angle_3_deg 11.507 r_dihedral_angle_1_deg 7.047 r_sphericity_bonded 6.963 r_rigid_bond_restr 2.867 r_long_range_B_refined 2.679 r_long_range_B_other 2.502 r_scangle_other 2.356 r_scbond_it 1.99 r_scbond_other 1.989 r_mcangle_other 1.708 r_mcangle_it 1.7 r_angle_refined_deg 1.552 r_mcbond_it 1.424 r_mcbond_other 1.325 r_angle_other_deg 1.244 r_chiral_restr 0.096 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.011 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 2030 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing