☰ Navigation Tabs
Open and closed conformations and protonation states of Candida antarctica Lipase B: atomic resolution native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TCA PDB ENTRY 1TCA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 CANDIDA ANTARCTICA LIPASE B (CALB) WAS PURCHASED BY HAMPTON RESEARCH AND CRYSTALLIZED WITHOUT FURTHER PURIFICATION. CRYSTALLIZATION TRIALS WERE PERFORMED AT 293 K USING THE HANGING-DROP METHOD USING A QUIAGEN EASYXTAL 15-WELL PLATE. 1 UL OF A 15 MG/ML CALB SOLUTION IN 20MM NA(CH3COO) PH = 4.8 WAS DILUTED WITH 1 UL OF THE PRECIPITANT SOLUTION, MADE OF 200MM NA(CH3COO) PH = 4.8, 20% (W/V) PEG4000, AND 10-13% (V/V) 2-PROPANOL. THE DROP WAS EQUILIBRATED BY VAPOR DIFFUSION AGAINST 500 ML OF THE PRECIPITANT SOLUTION. PROTEIN CRYSTALS OF NATIVE CALB APPEARED WITHIN ONE WEEK AND GREW TO A SIZE OF 0.2 X 0.4 X 0.5 MM3 IN THREE WEEKS.
Crystal Properties Matthews coefficient Solvent content 1.98 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.67 α = 88.74 b = 48.94 β = 97.15 c = 71.61 γ = 108.44
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 6M KB MIRRORS 2013-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) PETRA III, EMBL c/o DESY P13 (MX1)
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 0.91 71.04 94.5 0.11 13.65 17.2 343684 1.5
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 0.91 0.93 77.4 0.57 1.59 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TCA 0.91 71.04 326301 17383 94.48 0.11255 0.1115 0.1262 0.13197 0.1444 RANDOM 11.793
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] -0.04 -0.23 -0.1 0.4 0.16 -0.29
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.794 r_dihedral_angle_2_deg 33.317 r_dihedral_angle_4_deg 20.037 r_dihedral_angle_3_deg 11.303 r_sphericity_bonded 11.239 r_rigid_bond_restr 6.779 r_dihedral_angle_1_deg 6.583 r_angle_refined_deg 2.257 r_scbond_it 2.177 r_mcangle_it 1.565
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.794 r_dihedral_angle_2_deg 33.317 r_dihedral_angle_4_deg 20.037 r_dihedral_angle_3_deg 11.303 r_sphericity_bonded 11.239 r_rigid_bond_restr 6.779 r_dihedral_angle_1_deg 6.583 r_angle_refined_deg 2.257 r_scbond_it 2.177 r_mcangle_it 1.565 r_angle_other_deg 1.454 r_mcbond_it 1.324 r_mcbond_other 1.321 r_chiral_restr 0.159 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 r_gen_planes_other 0.009 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4632 Nucleic Acid Atoms Solvent Atoms 1019 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing