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Crystal structure of cutinase 1 from Thermobifida fusca DSM44342 (703)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 281 20 % PEG 3350,
0.02 M sodium / potassium phosphate,
0.1 M Bis-Tris propane pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.57 52.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.68 α = 90 b = 71.68 β = 90 c = 102.52 γ = 120
Symmetry Space Group P 32 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 PILATUS3 6M 2020-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.51 62.08 100 0.115 0.027 0.999 14.5 19.4 48462
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 1.51 1.54 100 3.682 0.852 0.35 0.9
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 4CG1 1.51 62.077 48416 2307 99.996 0.156 0.1542 0.1544 0.1855 0.1867 25.381
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] 0.041 0.021 0.041 -0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.004 r_dihedral_angle_4_deg 17.457 r_dihedral_angle_3_deg 11.068 r_dihedral_angle_1_deg 6.651 r_lrange_it 5.624 r_lrange_other 5.516 r_scangle_it 3.943 r_scangle_other 3.941 r_scbond_other 2.627 r_scbond_it 2.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.004 r_dihedral_angle_4_deg 17.457 r_dihedral_angle_3_deg 11.068 r_dihedral_angle_1_deg 6.651 r_lrange_it 5.624 r_lrange_other 5.516 r_scangle_it 3.943 r_scangle_other 3.941 r_scbond_other 2.627 r_scbond_it 2.625 r_mcangle_it 2.431 r_mcangle_other 2.43 r_angle_refined_deg 2.044 r_mcbond_it 1.617 r_angle_other_deg 1.614 r_mcbond_other 1.608 r_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.19 r_xyhbond_nbd_refined 0.189 r_symmetry_nbd_other 0.182 r_nbd_other 0.18 r_symmetry_nbd_refined 0.179 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_other 0.108 r_chiral_restr 0.107 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2018 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing