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Crystal structure of human carbonic anhydrase isozyme XII with the inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JD0 PDB ENTRY 1JD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 0.1M ammonium citrate with pH 5.0 and 16% of PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.709 α = 81.78 b = 67.261 β = 84.01 c = 80.689 γ = 86.48
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm Mirror Bent, vertically focussing 2011-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8123 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.45 27.164 97.1 0.039 0.039 14.1 4 166179 11.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.53 95.6 0.219 0.219 3.4 4 23905
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1JD0 1.45 26.5 166179 166177 16455 97.08 0.154 0.154 0.15 0.1476 0.188 0.1851 RANDOM 12.981
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] -0.33 0.05 0.02 -0.1 0.49 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.671 r_dihedral_angle_4_deg 18.181 r_dihedral_angle_3_deg 13.132 r_dihedral_angle_1_deg 7.373 r_scangle_it 4.448 r_scbond_it 3.129 r_angle_refined_deg 2.462 r_mcangle_it 2.214 r_mcbond_it 1.432 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.671 r_dihedral_angle_4_deg 18.181 r_dihedral_angle_3_deg 13.132 r_dihedral_angle_1_deg 7.373 r_scangle_it 4.448 r_scbond_it 3.129 r_angle_refined_deg 2.462 r_mcangle_it 2.214 r_mcbond_it 1.432 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.228 r_chiral_restr 0.2 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.167 r_metal_ion_refined 0.037 r_bond_refined_d 0.031 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8392 Nucleic Acid Atoms Solvent Atoms 1504 Heterogen Atoms 165
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PDB_EXTRACT data extraction DNA data collection MOLREP phasing