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Structure of thermolysin prepared by the 'soak-and-freeze' method under 40 bar of krypton pressure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DO1 PDB ENTRY 3DO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 1:1 WITH 50MM MES PH6, 1MNACL 45%(V/V) DMSO RESERVOIR: 35% SATURATED AMONIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.749 α = 90 b = 92.749 β = 90 c = 128.995 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS PILATUS 6M MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.5 46.37 99.5 0.08 34.3 34.9 52712 7.9 14.11
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 1.5 1.59 98.8 0.64 6.7 35.2
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3DO1 1.5 46.375 1.34 52712 2582 99.55 0.1624 0.1615 0.1623 0.1796 0.1797 15.8
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.252 f_angle_d 1.193 f_chiral_restr 0.046 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2432 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing