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Tetragonal thermolysin in the presence of betaine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L3F PDB entry 1L3F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 100 mg/mL protein in 45% DMSO, Mixing solution 45% DMSO, 1 M NaCl, 1 M ZnCl2, 0.1 M MES pH 6.0, Well 30% saturated AmSO4, Soak done in 3 M TMAO, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.53 65.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.149 α = 90 b = 96.149 β = 90 c = 105.099 γ = 90
Symmetry Space Group P 41 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 100 CCD OXFORD ONYX CCD 2011-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 20.082 99.9 0.118 14 8.6 33919 33919
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 2 2.11 100 0.564 0.564 1.3 5.6
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 (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 1L3F 2 20.08 33919 32146 1717 99.85 0.16243 0.16104 0.1628 0.1882 0.1901 RANDOM 19.44
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] -0.22 -0.22 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.371 r_dihedral_angle_4_deg 15.992 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 5.904 r_scangle_it 3.921 r_scbond_it 2.585 r_angle_refined_deg 1.615 r_mcangle_it 1.564 r_mcbond_it 0.905 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.371 r_dihedral_angle_4_deg 15.992 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 5.904 r_scangle_it 3.921 r_scbond_it 2.585 r_angle_refined_deg 1.615 r_mcangle_it 1.564 r_mcbond_it 0.905 r_chiral_restr 0.129 r_bond_refined_d 0.019 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2428 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 62
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data collection CrysalisPro data reduction