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The Crystal Structure of Leaf-branch compost cutinase from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6THT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.6M imidazole, 0.1M tri-sodium citrate PH7.8
Crystal Properties Matthews coefficient Solvent content 2.04 39.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.412 α = 90 b = 109.412 β = 90 c = 35.137 γ = 120
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 RIGAKU SATURN 944+ 2020-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 2.15 47.38 98.1 0.101 22.1 11 13146
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 2.15 2.22 0.262
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6tht 2.15 47.38 13144 678 98.082 0.183 0.1803 0.1914 0.2273 0.2342 9.937
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] -0.15 -0.075 -0.15 0.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.642 r_dihedral_angle_4_deg 12.029 r_dihedral_angle_3_deg 10.403 r_dihedral_angle_1_deg 6.508 r_lrange_it 1.664 r_lrange_other 1.664 r_angle_refined_deg 1.2 r_angle_other_deg 1.125 r_mcangle_it 0.373 r_mcangle_other 0.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.642 r_dihedral_angle_4_deg 12.029 r_dihedral_angle_3_deg 10.403 r_dihedral_angle_1_deg 6.508 r_lrange_it 1.664 r_lrange_other 1.664 r_angle_refined_deg 1.2 r_angle_other_deg 1.125 r_mcangle_it 0.373 r_mcangle_other 0.373 r_scangle_it 0.293 r_scangle_other 0.293 r_mcbond_it 0.202 r_mcbond_other 0.201 r_nbd_other 0.184 r_nbd_refined 0.183 r_symmetry_nbd_other 0.167 r_scbond_it 0.161 r_nbtor_refined 0.15 r_scbond_other 0.149 r_xyhbond_nbd_refined 0.123 r_symmetry_xyhbond_nbd_refined 0.098 r_symmetry_nbd_refined 0.084 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.043 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1948 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing