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Crystal structure of a cutinase enzyme from Saccharopolyspora flava (611)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20 % PEG 3350,
0.2 M sodium fluoride,
0.1 M Bis-Tris propane pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.94 58.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.336 α = 90 b = 89.336 β = 90 c = 74.324 γ = 120
Symmetry Space Group P 3 2 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 2021-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.8153 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 1.561 77.367 94.9 0.14 0.034 0.999 12.5 17.4 40562
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 1.561 1.652 2.153 0.548 0.632 1.4
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 1jfr 1.561 77.367 40562 1981 82.749 0.142 0.1406 0.1385 0.1653 0.1641 21.693
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] 0.013 0.007 0.013 -0.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.092 r_dihedral_angle_3_deg 11.036 r_dihedral_angle_4_deg 8.956 r_dihedral_angle_1_deg 6.804 r_lrange_it 5.877 r_lrange_other 5.576 r_scangle_it 2.738 r_scangle_other 2.737 r_angle_refined_deg 2.013 r_scbond_it 1.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.092 r_dihedral_angle_3_deg 11.036 r_dihedral_angle_4_deg 8.956 r_dihedral_angle_1_deg 6.804 r_lrange_it 5.877 r_lrange_other 5.576 r_scangle_it 2.738 r_scangle_other 2.737 r_angle_refined_deg 2.013 r_scbond_it 1.886 r_scbond_other 1.885 r_mcangle_other 1.768 r_mcangle_it 1.761 r_angle_other_deg 1.617 r_mcbond_it 1.17 r_mcbond_other 1.118 r_symmetry_xyhbond_nbd_other 0.555 r_symmetry_xyhbond_nbd_refined 0.277 r_symmetry_nbd_refined 0.253 r_xyhbond_nbd_refined 0.237 r_nbd_refined 0.223 r_symmetry_nbd_other 0.181 r_nbd_other 0.178 r_nbtor_refined 0.175 r_chiral_restr 0.108 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1949 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing