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Tetragonal thermolysin in the presence of sarcosine
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 4 M sarcosine, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.58 65.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.346 α = 90 b = 96.346 β = 90 c = 105.875 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 2011-04-28 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 2.1 20.221 99.9 0.13 11.4 6 29727 29727
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 2.1 2.21 100 0.59 0.59 1.3 4
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 2.1 20.22 29727 28165 1505 99.82 0.17518 0.17307 0.1758 0.21558 0.2151 RANDOM 18.229
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] -0.27 -0.27 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.136 r_dihedral_angle_4_deg 24.254 r_dihedral_angle_3_deg 12.943 r_dihedral_angle_1_deg 5.896 r_scangle_it 4.407 r_scbond_it 2.913 r_angle_refined_deg 1.735 r_mcangle_it 1.625 r_mcbond_it 0.934 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.136 r_dihedral_angle_4_deg 24.254 r_dihedral_angle_3_deg 12.943 r_dihedral_angle_1_deg 5.896 r_scangle_it 4.407 r_scbond_it 2.913 r_angle_refined_deg 1.735 r_mcangle_it 1.625 r_mcbond_it 0.934 r_chiral_restr 0.121 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 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 194 Heterogen Atoms 36
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data collection CrysalisPro data reduction