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Crystal structure of cutinase PsCut from Pseudomonas saudimassiliensis
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, SITTING DROP 293 0.1 M sodium acetate pH 4.6,
8% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.02 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.786 α = 90 b = 56.813 β = 121.627 c = 105.796 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M-F 2017-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 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 1.56 52.38 98.9 0.092 0.04 0.998 9 4.7 113320
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 1.56 1.59 93.7 0.507 0.449 0.473 1.1 1.9
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 1.56 52.377 112473 5514 98.292 0.179 0.1779 0.19 0.203 0.2108 21.566
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] -0.408 0.103 0.568 -0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.886 r_dihedral_angle_3_deg 12.615 r_dihedral_angle_2_deg 12.458 r_dihedral_angle_1_deg 6.824 r_lrange_it 5.948 r_lrange_other 5.845 r_scangle_it 2.573 r_scangle_other 2.573 r_mcangle_it 2.017 r_mcangle_other 2.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.886 r_dihedral_angle_3_deg 12.615 r_dihedral_angle_2_deg 12.458 r_dihedral_angle_1_deg 6.824 r_lrange_it 5.948 r_lrange_other 5.845 r_scangle_it 2.573 r_scangle_other 2.573 r_mcangle_it 2.017 r_mcangle_other 2.017 r_scbond_it 1.67 r_scbond_other 1.664 r_angle_refined_deg 1.458 r_mcbond_it 1.266 r_mcbond_other 1.263 r_angle_other_deg 0.528 r_symmetry_nbd_refined 0.348 r_nbd_other 0.239 r_symmetry_xyhbond_nbd_other 0.23 r_xyhbond_nbd_refined 0.219 r_nbd_refined 0.214 r_symmetry_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.18 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.079 r_ncsr_local_group_1 0.077 r_ncsr_local_group_2 0.07 r_ncsr_local_group_3 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6104 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing