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Controlled lid-opening in Thermomyces lanuginosus lipase - a switch for activity and binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DT3 PDB ENTRY 1DT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 50 % PEG400, 0.2 M LITHIUM SULFATE, 0.1 M NA-ACETATE PH 4.5, SITTING DROP, VAPOUR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.478 α = 90 b = 90.478 β = 90 c = 160.455 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 2015-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.8 50.02 99.9 0.07 20.9 13.1 59391 2
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 1.8 1.84 97.7 0.87 3 12.8
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 1DT3 1.8 50.02 59391 3061 99.84 0.17272 0.17152 0.1829 0.19693 0.2065 RANDOM 36.267
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] 0.4 0.4 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 15.232 r_dihedral_angle_3_deg 12.325 r_dihedral_angle_1_deg 6.256 r_mcangle_it 1.769 r_angle_refined_deg 1.706 r_scbond_it 1.65 r_angle_other_deg 1.497 r_mcbond_it 1.125 r_mcbond_other 1.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 15.232 r_dihedral_angle_3_deg 12.325 r_dihedral_angle_1_deg 6.256 r_mcangle_it 1.769 r_angle_refined_deg 1.706 r_scbond_it 1.65 r_angle_other_deg 1.497 r_mcbond_it 1.125 r_mcbond_other 1.125 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4061 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing