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Structure of Thermolysin solved from SAD data collected at the peak of the Zn absorption edge on ID30B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.05M MES, 1M NaCl, 45% DMSO
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.717 α = 90 b = 92.717 β = 90 c = 128.621 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 2017-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.282 ESRF ID30B
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 1.43 80.3 96.7 0.079 0.096 0.042 0.99 13.6 2.8 60230 11.3
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 1.43 1.45 79.1 0.203 0.262 0.137 0.93 3.7 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.43 80.3 57172 3000 98.68 0.14523 0.14425 0.16405 0.2174 RANDOM 16.417
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] -0.07 -0.04 -0.07 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.359 r_dihedral_angle_4_deg 15.475 r_dihedral_angle_3_deg 12.1 r_dihedral_angle_1_deg 5.591 r_long_range_B_refined 4.381 r_long_range_B_other 4.175 r_scangle_other 2.327 r_scbond_it 2.036 r_scbond_other 2.035 r_angle_refined_deg 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.359 r_dihedral_angle_4_deg 15.475 r_dihedral_angle_3_deg 12.1 r_dihedral_angle_1_deg 5.591 r_long_range_B_refined 4.381 r_long_range_B_other 4.175 r_scangle_other 2.327 r_scbond_it 2.036 r_scbond_other 2.035 r_angle_refined_deg 1.71 r_mcangle_it 1.342 r_mcangle_other 1.342 r_mcbond_it 1.066 r_angle_other_deg 1.044 r_mcbond_other 1.039 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2449 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling CRANK2 phasing