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Mimic carbonic anhydrase IX in complex with Methyl 2-chloro-4-(cyclohexylsulfanyl)-5-sulfamoylbenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Crystallization buffer: 0.1M sodium bicine (pH 9.0), 0.2 M ammonium sulfate and 2M sodium malonate (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.08 40.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.06 α = 90 b = 41.348 β = 104.14 c = 72.029 γ = 90
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 2013-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9755 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 1.12 41.35 81.3 0.042 0.063 0.032 18.9 3.8 146352
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.122 1.18 51.4 0.102 0.102 0.153 0.079 6.7 3.6
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 3HLJ 1.12 41.35 131858 14494 81.32 0.1637 0.1603 0.1605 0.1937 0.1938 RANDOM 18.286
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] 1.47 1.03 -0.41 -0.41 0.96 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.027 r_sphericity_free 28.405 r_sphericity_bonded 25.223 r_rigid_bond_restr 20.997 r_dihedral_angle_4_deg 20.67 r_dihedral_angle_3_deg 14.895 r_dihedral_angle_1_deg 7.172 r_angle_refined_deg 2.532 r_chiral_restr 0.52 r_bond_refined_d 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.027 r_sphericity_free 28.405 r_sphericity_bonded 25.223 r_rigid_bond_restr 20.997 r_dihedral_angle_4_deg 20.67 r_dihedral_angle_3_deg 14.895 r_dihedral_angle_1_deg 7.172 r_angle_refined_deg 2.532 r_chiral_restr 0.52 r_bond_refined_d 0.02 r_gen_planes_refined 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4079 Nucleic Acid Atoms Solvent Atoms 602 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing Coot model building