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Crystal structure of cutinase RgCutII from Rhizobacter gummiphilus
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 HEPES pH 7.5,
1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.09 41.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.127 α = 90 b = 63.127 β = 90 c = 222.746 γ = 120
Symmetry Space Group P 61 2 2
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 2018-03-11 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 1.08 49.08 99.4 0.068 0.024 0.999 11.7 8.7 112681
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 1.08 1.1 96.3 0.774 0.44 0.555 1.8 6
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 1.08 49.076 104451 5265 92.16 0.199 0.1978 0.1977 0.214 0.2139 12.965
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] 0.466 0.233 0.466 -1.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.66 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_2_deg 10.686 r_dihedral_angle_1_deg 6.252 r_lrange_it 4.851 r_lrange_other 4.569 r_scangle_it 2.046 r_scangle_other 2.046 r_angle_refined_deg 1.841 r_scbond_it 1.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.66 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_2_deg 10.686 r_dihedral_angle_1_deg 6.252 r_lrange_it 4.851 r_lrange_other 4.569 r_scangle_it 2.046 r_scangle_other 2.046 r_angle_refined_deg 1.841 r_scbond_it 1.376 r_scbond_other 1.376 r_mcangle_other 1.322 r_mcangle_it 1.321 r_mcbond_it 0.842 r_mcbond_other 0.836 r_angle_other_deg 0.638 r_symmetry_xyhbond_nbd_refined 0.245 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.185 r_nbd_other 0.164 r_symmetry_nbd_refined 0.133 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.011 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 1920 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing