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Crystal structure of human carbonic anhydrase II in complex with Benzoxaborole at pH=8.7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 298 SODIUM CITRATE 1.3M, TRIS-HCL 0.1M
Crystal Properties Matthews coefficient Solvent content 2.1 41.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.35 α = 90 b = 41.19 β = 104.4 c = 72.03 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 CCD RIGAKU SATURN 944 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 1.4 50 89.1 0.037 31.8 4.5 42313
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 1.4 1.42 74.2 0.21 5.7 3.5
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 FOURIER SYNTHESIS THROUGHOUT 1CA2 1.4 50 39512 2082 87.51 0.1075 0.1054 0.1059 0.1461 0.1458 RANDOM 13.898
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] 0.13 0.31 -0.3 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.486 r_sphericity_free 25.373 r_dihedral_angle_4_deg 25.047 r_dihedral_angle_3_deg 10.995 r_sphericity_bonded 9.968 r_dihedral_angle_1_deg 6.523 r_rigid_bond_restr 2.673 r_mcangle_it 2.202 r_mcbond_it 1.807 r_angle_refined_deg 1.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.486 r_sphericity_free 25.373 r_dihedral_angle_4_deg 25.047 r_dihedral_angle_3_deg 10.995 r_sphericity_bonded 9.968 r_dihedral_angle_1_deg 6.523 r_rigid_bond_restr 2.673 r_mcangle_it 2.202 r_mcbond_it 1.807 r_angle_refined_deg 1.805 r_mcbond_other 1.797 r_angle_other_deg 0.836 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 23
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing CrystalClear data collection HKL-2000 data reduction