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Open and closed conformations and protonation states of Candida antarctica Lipase B: Xenon complex
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 = 39.656 α = 87.8 b = 48.89 β = 98.07 c = 71.68 γ = 108.17
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 2013-03-25 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 2.27 70.96 92.7 0.06 29.5 6.2 21330 7
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 2.27 2.36 70.5 0.34 7.2 4.6
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 PDB ENTRY 1TCA 2.28 70.97 20233 1097 92.18 0.14226 0.1393 0.1397 0.1948 0.1945 RANDOM 14.381
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] 0.05 0.17 -0.11 0.01 -0.2 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.209 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_3_deg 13.606 r_dihedral_angle_1_deg 6.235 r_scbond_it 1.585 r_mcangle_it 1.53 r_angle_refined_deg 1.416 r_mcbond_it 1.021 r_chiral_restr 0.08 r_bond_refined_d 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.209 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_3_deg 13.606 r_dihedral_angle_1_deg 6.235 r_scbond_it 1.585 r_mcangle_it 1.53 r_angle_refined_deg 1.416 r_mcbond_it 1.021 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4639 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing