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Crystal structure of leaf branch compost cutinase variant
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 MICROBATCH 293 10 mM Tris, 150 mM NaCl, 0.6 M succinic acid, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.83 67.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.91 α = 90 b = 101.87 β = 90 c = 265.81 γ = 90
Symmetry Space Group I 2 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 2023-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0000 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.007 48.955 100 0.998 7.98 10.34 919234
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.13 0.499
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.007 48.955 88905 4446 99.926 0.21 0.2079 0.2079 0.2498 0.25 46.189
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] 0.819 3.45 -4.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.232 r_dihedral_angle_6_deg 14.212 r_dihedral_angle_2_deg 9.471 r_lrange_it 9.389 r_dihedral_angle_1_deg 7.8 r_scangle_it 7.129 r_mcangle_it 6.216 r_scbond_it 5.319 r_mcbond_it 4.319 r_angle_refined_deg 1.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.232 r_dihedral_angle_6_deg 14.212 r_dihedral_angle_2_deg 9.471 r_lrange_it 9.389 r_dihedral_angle_1_deg 7.8 r_scangle_it 7.129 r_mcangle_it 6.216 r_scbond_it 5.319 r_mcbond_it 4.319 r_angle_refined_deg 1.912 r_nbtor_refined 0.316 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.157 r_symmetry_nbd_refined 0.146 r_chiral_restr 0.115 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5870 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing