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Human carbonic anhydrase IX mimic with Epacadostat bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G03 PDB entry 5G03
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 nL 5.9 mg/mL protein + 200 nL reservoir (2.7 M ammonium sulfate, 50 mM Tris buffer, pH 8.2)
Crystal Properties Matthews coefficient Solvent content 2.08 40.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.979 α = 90 b = 41.436 β = 104.117 c = 72.122 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 EIGER X 16M 2019-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953657 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.37 41.4 96.5 0.05 0.998 10.7 11.9 48966
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.39 91.2 0.469 0.63 6.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 5G03 1.37 40.744 48927 2424 96.12 0.129 0.1269 0.1261 0.1671 0.1661 14.28
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] 0.545 -0.128 -0.125 -0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.431 r_dihedral_angle_4_deg 20.038 r_dihedral_angle_3_deg 11.504 r_dihedral_angle_1_deg 6.805 r_lrange_it 3.391 r_lrange_other 3.201 r_scangle_it 2.879 r_scangle_other 2.874 r_rigid_bond_restr 2.493 r_scbond_other 2.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.431 r_dihedral_angle_4_deg 20.038 r_dihedral_angle_3_deg 11.504 r_dihedral_angle_1_deg 6.805 r_lrange_it 3.391 r_lrange_other 3.201 r_scangle_it 2.879 r_scangle_other 2.874 r_rigid_bond_restr 2.493 r_scbond_other 2.359 r_scbond_it 2.358 r_mcangle_it 2.221 r_mcangle_other 2.221 r_angle_refined_deg 1.772 r_mcbond_it 1.638 r_mcbond_other 1.623 r_angle_other_deg 1.481 r_nbd_refined 0.249 r_symmetry_nbd_refined 0.217 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.198 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.17 r_nbd_other 0.163 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2040 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing