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Crystal structure of a cutinase enzyme from Marinactinospora thermotolerans DSM45154 (606)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Sodium HEPES pH 7.5,
70% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.31 46.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.966 α = 90 b = 45.354 β = 108.193 c = 86.598 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 16M 2021-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.933 82.269 91.6 0.253 0.114 0.988 5.5 5.9 29683
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.933 2.097 52 1.343 0.555 0.577 1.4 6.7
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 4WFJ 1.933 82.269 29683 1448 71.91 0.235 0.2322 0.2313 0.282 0.2821 18.851
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] -0.485 0.121 -0.195 0.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.569 r_dihedral_angle_4_deg 17.485 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_1_deg 7.343 r_lrange_it 2.858 r_lrange_other 2.791 r_angle_refined_deg 1.74 r_angle_other_deg 1.342 r_scangle_it 1.205 r_scangle_other 1.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.569 r_dihedral_angle_4_deg 17.485 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_1_deg 7.343 r_lrange_it 2.858 r_lrange_other 2.791 r_angle_refined_deg 1.74 r_angle_other_deg 1.342 r_scangle_it 1.205 r_scangle_other 1.204 r_mcangle_other 1.156 r_mcangle_it 1.155 r_scbond_it 0.726 r_scbond_other 0.726 r_mcbond_it 0.682 r_mcbond_other 0.675 r_nbd_other 0.359 r_symmetry_nbd_refined 0.298 r_xyhbond_nbd_refined 0.216 r_nbd_refined 0.208 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_other 0.106 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.077 r_ncsr_local_group_1 0.053 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4044 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing