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X-Ray structure of Thermolysin crystallized on a silicon chip
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 0.1M MES-NaOH pH 6.5, 10mM calcium chloride, 25% PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.667 α = 90 b = 92.667 β = 90 c = 128.311 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 PILATUS3 6M 2018-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0 PETRA III, DESY P11
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 single crystalline silicon chip goniometer
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.733 46.334 100 0.168 0.175 0.048 0.995 11.4 13.2 34527 12.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.733 1.77 100 0.976 1.013 0.266 0.81 3.1 13.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 FREE R-VALUE 2TLX 1.733 46.334 1.34 34457 1571 99.97 0.1297 0.1283 0.13 0.1611 0.1627 16.57
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 10.964 f_angle_d 0.841 f_chiral_restr 0.051 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2432 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 210
Software Software Software Name Purpose PHENIX refinement Coot model building PHASER phasing PDB_EXTRACT data extraction Aimless data scaling XDS data reduction