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Crystal structure of a cutinase enzyme from Thermobifida fusca YX (705)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZOA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.05 M Cesium Chloride,
0.1 M MES pH 6.5,
30% (v/v) Jeffamine M-600
Crystal Properties Matthews coefficient Solvent content 2.07 40.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.164 α = 90 b = 150.212 β = 92.509 c = 43.396 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 PILATUS 6M-F 2020-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9119 Diamond I04-1
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 1.429 75.106 89 0.121 0.049 0.997 9.3 6.9 57020
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 1.429 1.582 55.7 1.17 0.493 0.567 1.5 6.4
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 5zoa 1.429 75.106 57020 2826 64.38 0.183 0.1817 0.1822 0.2158 0.2165 16.01
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] 0.008 0.019 -0.281 0.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.253 r_dihedral_angle_4_deg 18.672 r_dihedral_angle_3_deg 11.169 r_dihedral_angle_1_deg 7.319 r_lrange_it 4.323 r_lrange_other 4.184 r_scangle_it 2.417 r_scangle_other 2.417 r_angle_refined_deg 1.857 r_mcangle_other 1.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.253 r_dihedral_angle_4_deg 18.672 r_dihedral_angle_3_deg 11.169 r_dihedral_angle_1_deg 7.319 r_lrange_it 4.323 r_lrange_other 4.184 r_scangle_it 2.417 r_scangle_other 2.417 r_angle_refined_deg 1.857 r_mcangle_other 1.828 r_mcangle_it 1.827 r_scbond_it 1.551 r_scbond_other 1.551 r_angle_other_deg 1.539 r_mcbond_it 1.173 r_mcbond_other 1.166 r_symmetry_xyhbond_nbd_refined 0.259 r_nbd_refined 0.228 r_symmetry_nbd_refined 0.219 r_xyhbond_nbd_refined 0.21 r_nbd_other 0.21 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_other 0.191 r_nbtor_refined 0.179 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_1 0.07 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3982 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing